FISH PASSAGE CENTER 2013 ANNUAL REPORT DRAFT

Transcription

1 FISH PASSAGE CENTER 2013 ANNUAL REPORT DRAFT This report responds to the Fish Passage Center annual reporting requirements to the Northwest Power and Conservation Council under its Columbia River Basin Fish and Wildlife Program and the annual reporting requirements to the Bonneville Power Administration under its funding contracts which supported this work. BPA Contract # BPA Project # /1/13 to 12/31/13 Michele DeHart Fish Passage Center Manager Fish Passage Center 847 NE 19 th Avenue, #250 Portland, Oregon May 30, 2014

2 2013 Fish Passage Center Annual Report Table of Contents List of Appendices...v List of Tables... vi List of Figures...x List of Maps...xv Executive Summary... xvi I. Introduction...1 II. Water Supply...3 A. Water Supply...3 B. Water Supply/Management Impacts to Biological Opinion Measures Grand Coulee Dam Dworshak Dam Libby Dam Hungry Horse Dam Brownlee Dam...12 C. Spring/Summer Flow Objectives...13 D. Dworshak Dam Summer Operations for Temperature Regulation at Lower Granite Dam...17 E. Canadian Operations...19 F. Snake River...19 G. Summary...19 III Spill Management...22 A. Spill Overview Spill Planning and Operations Project-Specific Operations Summary and Conclusions...47 B. Gas Bubble Trauma (GBT) Monitoring and Data Reporting for Overview...47 Draft 2013 Annual Report i May 2014

3 2. Results Discussion...57 IV Smolt Monitoring...60 A. Summary...60 B. Special Operations at Sites in the Lower Snake and Lower Columbia in Lower Granite Dam (LGR) Little Goose Dam (LGS) Lower Monumental Dam (LMN) Ice Harbor Dam (IHR) McNary Dam (MCN) John Day Dam (JDA) The Dalles Dam (TDA) Bonneville Dam (BON)...64 C. Overview of Travel Time and Survival Under 2013 Conditions Snake River Mid Columbia River Lower Columbia River...64 D. Smolt Monitoring Sites and Schedules for 2013 and Methods for Analyses Smolt Monitoring Sites and Schedules for Methods: Collection Estimates and Passage Index Methods: Population Index Methods: Population Estimate Methods: Summary of Mortality, Descaling, and Injury Data from SMP Methods: Reach Survival Estimation using PIT-Tag Mark-Recapture Methods: Estimation of Fish Travel Time Methods: Environmental Variables Assigned to Survival Cohorts Methods: Relative Migration Rate...72 E. Results: Collection Estimates, Relative Abundance and Population Indices Snake River Columbia River...78 F. Results: Migration Timing...80 G. Results: Summary of Mortality, Descaling, and Injury Data from SMP Mortality Descaling Injury...85 H. Results: Travel Time and Survival Analyses for Hatchery and Trap Releases Snake River Traps Mid-Columbia Hatcheries...89 Draft 2013 Annual Report ii May 2014

4 I. Results: Reach Survival Analyses Introduction Lower Granite Dam to McNary Dam McNary Dam to Bonneville Dam Rock Island Dam to McNary Dam Reach Survival...98 J. Overall Conclusions from SMP Chapter K. Literature Cited V Adult Fish Passage A. Introduction B. Adult Counting Procedures C. General Life Histories D. Variables Affecting Dam Counts E Passage Conditions Water Temperature Adult Facilities Inspection Program F. Adult Fish Counts/Conclusions Spring Chinook Summer Chinook Fall Chinook Coho Sockeye Steelhead Lamprey Pink and Chum G. Predicted Run Sizes I. Adult Section References VI Columbia River Basin Hatchery Releases of Anadromous Salmon Species A. General Overview of Hatchery Section B. General Overview of 2013 Releases Fall Chinook Spring Chinook Summer Chinook Coho Sockeye Steelhead Cutthroat Trout and Chum Draft 2013 Annual Report iii May 2014

5 C. Below Bonneville Dam Zone Fall Chinook Spring Chinook Coho Steelhead Chum and Cutthroat Trout D. Lower Columbia River Zone Fall Chinook Spring Chinook Coho Steelhead E. Mid-Columbia River Zone Fall Chinook Spring Chinook Summer Chinook Coho Sockeye Steelhead F. Snake River Zone Fall Chinook Spring Chinook Summer Chinook Coho Sockeye Steelhead G. Egg, Fry, and Adult Releases Below Bonneville Dam Zone Lower Columbia Zone Mid-Columbia Zone Snake River Zone H. Conclusion Draft 2013 Annual Report iv May 2014

6 List of Appendices Appendix A Appendix B Appendix C Appendix D Appendix E Appendix F Appendix G Appendix H Appendix I Appendix J Appendix K Appendix L Memorandums and Other Documents 2013 Total Dissolved Gas Saturation Plots Gas Bubble Trauma and Total Dissolved Gas Saturation Migration Timing Plots Travel Time Tables Hatchery Release Schedule Transportation Proportion Tables Data Tables for Chapter 4 SMP Multi-Year Reach Survival and Fish Travel Time Analyses Summary of Mortality, Descaling, and Injury Data From SMP 2013 System Operational Requests (SORs) 2013 Joint Technical Staff Letters Web Statistics and Data Request Summaries Appendix M Project Locations and Individual Project Schematics Appendix N Acronyms Draft 2013 Annual Report v May 2014

7 List of Tables Table 2.1. January and March Final Water Supply Forecasts and observed runoff at The Dalles, Grand Coulee, Lower Granite, Libby, Dworshak, and Hungry Horse dams over various time periods in WY Table 2.2. Observed Runoff at Lower Granite Dam and The Dalles Dam from January July from 1991 to 2013 along with each year s rank in terms of the 85-year record between 1929 and 2013 (lower rank = higher water year)....4 Table 2.3. Individual month and Water Year 2013 precipitation from October 1, 2012, to September 30, 2013, at select locations within the Columbia Basin in percent of normal ( )...5 Table 2.4. Seasonal snow water equivalents at select basins during various points of Water Year 2013 Data from ftp://ftp.wcc.nrcs.usda.gov/data/snow/update/columbia/....6 Table 2.5. April 10 th Biological Opinion Flood Control Elevations at Grand Coulee, Libby, Dworshak, Hungry Horse, and Brownlee along with actual elevations on April 10, Table 2.6. Spring and summer flow averages at Lower Granite, McNary, and Priest Rapids dams during their respective spring and summer Biological Opinion periods Table 2.7. Spring and summer weekly flow averages at Lower Granite, McNary, and Priest Rapids dams during the 2013 spring and summer Biological Opinion periods Table 3.1. Planned spill levels for the FCRPS during spring and summer Table 3.2. Ranking criteria used in monitoring for signs of gas bubble trauma Table 3.3. Number of juvenile salmonids examined for signs of GBT at dams on the Lower Snake River and on the Columbia River from April to August 2013 as part of the GBT Monitoring Program Table 3.4. Number of juvenile salmonids found with fin GBT at dams on the Lower Snake River and on the Columbia River from April to August 2013 as part of the GBT Monitoring Program Table 3.5. Percent of sampled fish with signs of fin GBT estimated for the total fish observed in each year 1996 to Table 4.1. Smolt monitoring sites and schedules for Table 4.2. Formulas to compute passage indices (collection estimate/flow expansion factor) at dams Table 4.3. Collection counts of composite wild/hatchery Chinook, steelhead, coho, and sockeye at the four traps used in the Smolt Monitoring Program in Table 4.4. Comparison of sample, collection estimates, and passage indices of salmonids and larval and juvenile lamprey at Snake River dams in 2013 with recent annual passage indices Table 4.5. Hatchery yearling Chinook population estimates and indices at Lower Granite Dam in 2013 compared to recent years Draft 2013 Annual Report vi May 2014

8 Table 4.6. Wild and unmarked yearling Chinook population estimates and indices at Lower Granite Dam in 2013 compared to recent years Table 4.7. Hatchery steelhead population estimates and indices at Lower Granite Dam in 2013 compared to recent years Table 4.8. Wild and unmarked hatchery steelhead population estimates and indices at Lower Granite Dam in 2013 compared to recent years...77 Table 4.9. Sample, collection, and passage indices of salmonids and larval and juvenile lamprey at Columbia River dams in 2013and comparison with 2010 to 2012 annual passage indices Table Migration timing of salmonids and larval and juvenile Pacific lamprey at Lower Granite, Rock Island, McNary, and John Day dams in 2013 compared to 2012 and 2011 and the 10-year average ( ) Table Median travel time and flow for hatchery (H) and wild (W) yearling Chinook and steelhead released from traps on the Salmon, Imnaha, Grande Ronde, and Snake rivers to Lower Granite Dam in 2013 compared to other recent years Table Annual reach survival estimates of Snake River basin PIT-tagged yearling Chinook from trap release sites to Lower Monumental Dam tailrace for years 2008 to Table Annual reach survival estimate of Snake River basin PIT tagged steelhead from trap release sites to Lower Monumental Dam tailrace in the years 2008 to Table Median travel time for Mid-Columbia River hatchery Chinook from hatchery site to McNary Dam in 2013 compared to 2010 to Flows at Priest Rapids Dam were used as an index of total discharge each year in the reaches Table Annual average reach survival estimates of Mid-Columbia River basin PIT-tagged yearling and subyearling hatchery Chinook from release site to McNary Dam tailrace in the years 2007 to Table 5.1. Columbia and Snake River dam completion dates location (individual project schematics in Appendix L) Table Adult dam count monitoring dates Table 5.3. Columbia River Salmon and Steelhead Populations Upstream of Bonneville Dam Table Major CRB salmonid fisheries Table 5.5. Number of days 2013 water temperature > 68 o F Table 5.6a Spring Chinook Cumulative 2013 Adult Passage at Mainstem Dams Table 5.6b Summer Chinook Cumulative 2013 Adult Passage at Mainstem Dams Table 5.6c Fall Chinook Cumulative 2013 Adult Passage at Mainstem Dams Table 5.6d Coho Cumulative 2013 Adult Passage at Mainstem Dams Table 5.6e Sockeye Cumulative 2013 Adult Passage at Mainstem Dams Table 5.6f Steelhead Cumulative 2013 Adult Passage at Mainstem Dams Table 5.7a 2013 Adult Spring Chinook Run Duration at Bonneville Dam Table 5.7b 2013 Adult Summer Chinook Run Duration at Bonneville Dam Draft 2013 Annual Report vii May 2014

9 Table 5.7c 2013 Adult Fall Chinook Run Duration at Bonneville Dam Table 5.7d 2013 Adult Coho Run Duration at Bonneville Dam Table 5.7e 2013 Adult Sockeye Run Duration at Bonneville Dam Table 5.7f 2013 Adult Steelhead Run Duration at Bonneville Dam Table 5.8. TAC 2013 run size forecast and actual returns Table 6.1. Hatchery release totals by River Zone: Snake River, Mid-Columbia River (above McNary Dam), Lower Columbia River (Bonneville Dam to McNary Dam), and Below Bonneville Dam intended for out-migration in Table 6.2. Total number of anadromous salmon species released into the Below Bonneville River Zone for out-migration in 2013 that were released unmarked Table 6.3. Hatchery release totals for the Below Bonneville Dam River Zone, Table 6.4. Hatchery release totals for the Lower Columbia River Zone, Table 6.5. Total number of anadromous salmon species released into the Lower Columbia River Zone for out-migration in 2013 that were released unmarked Table 6.6. Hatchery release totals for the Mid-Columbia River Zone, Table 6.7. Total number of anadromous salmon species released into the Mid-Columbia River Zone for out-migration in 2013 that were released unmarked Table 6.8. Hatchery release totals for the Snake River Zone, Table 6.9. Total number of anadromous salmon species released into the Snake River Zone for out-migration in 2013 that were released unmarked Table Snake and Clearwater River subyearling fall Chinook release dates and release time spans from Draft 2013 Annual Report viii May 2014

10 List of Figures Figure 2.1 Operations at Grand Coulee Dam over WY Figure 2.2. Operations at Dworshak Dam over WY Figure 2.3. Operations at Libby Dam over WY Figure 2.4. Operations at Hungry Horse Dam over WY Figure 2.5. Operations at Brownlee Dam over WY Figure 2.6. Spring and summer Biological Opinion flow objectives and actual flows at McNary Dam over the BiOp period Figure 2.7. Spring and summer Biological Opinion flow objectives and actual flows at Lower Granite Dam over the BiOp period Figure 2.8. Spring Biological Opinion flow objectives and actual flows at Priest Rapids Dam over the BiOp period Figure 2.9. Tailwater temperature and temperature standard at Lower Granite Dam as well as the temperature and magnitude of discharges from Dworshak Dam from July 1 to September 30, Figure 3.1. Dworshak (DR) Dam flow and spill for spring and summer of Figure 3.2. Lower Granite Dam (LGR) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure 3.3. Historic spill at Lower Granite Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure 3.4. Little Goose Dam (LGS) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure 3.5. Historic spill at Little Goose Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure 3.6. Lower Monumental Dam (LMN) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure 3.7. Historic spill at Lower Monumental Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure 3.8. Ice Harbor Dam (IHR) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure 3.9. Historic spill at Ice Harbor Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure McNary Dam (MCN) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure Historic spill at McNary Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure John Day Dam (JDA) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Draft 2013 Annual Report ix May 2014

11 Figure Historic spill at John Day Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure The Dalles Dam (TDA) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure Historic spill at The Dalles Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure Bonneville Dam (BON) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure Historic spill at Bonneville Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period Figure Grand Coulee Dam daily average flow and actual spill levels for spring and summer of Figure Chief Joseph Dam daily average flow and actual spill levels for spring and summer of Figure Wells Dam daily average flow and actual spill levels for spring and summer of Figure Historic spill at Wells Dam as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period Figure Rocky Reach Dam daily average flow and actual spill levels for spring and summer of Figure Historic spill at Rocky Reach Dam as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period Figure Rock Island Dam daily average flow and actual spill levels for spring and summer of Figure Historic spill at Rock Island Dam as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period Figure Wanapum Dam daily average flow and actual spill levels for spring and summer of Figure Historic spill as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period Figure Priest Rapids Dam flow and actual spill levels for spring and summer of Figure Historic spill as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period Figure Average daily flows at Lower Granite Dam 2013, 2012, and the 10-year average Figure Average daily flows at McNary Dam 2013, 2012, and the 10-year average Figure Percent GBT observed in the sample at Lower Granite Dam...51 Figure Percent GBT observed in the sample at Little Goose Dam Figure Percent GBT observed in the sample at Lower Monumental Dam Figure Percent GBT observed in the sample at McNary Dam Figure Percent GBT observed in the sample at Bonneville Dam Draft 2013 Annual Report x May 2014

12 Figure Percent GBT observed in the sample at Rock Island Dam Figure 4.1. Daily descaling rates of subyearling Chinook at LGR in 2013, 2012 and the 10-year average ( )...84 Figure 4.2. Hatchery Yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Figure 4.3. Wild Yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Figure 4.4. Hatchery subyearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Figure 4.5. Combined hatchery and wild steelhead survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Figure 4.6. Hatchery sockeye survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Figure 4.7. Combined hatchery and wild yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the MCN to BON reach for migration years 1999 to Figure 4.8. Combined hatchery and wild steelhead survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the MCN to BON reach for migration years 1999 to Figure 4.9. Yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Figure Steelhead survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Figure Subyearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Figure Sockeye survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Figure 5.1a Bonneville Dam average daily water temperature Draft 2013 Annual Report xi May 2014

13 Figure 5.1b McNary Dam average daily water temperature Figure 5.1c Lower Granite Dam average daily water temperature Figure 5.1d Priest Rapids Dam average daily water temperature Figure 5.1e Rock Island Dam average daily water temperature Figure 5.2. Spring Chinook Adult Passage Figure 5.3. Spring Chinook Jack Passage Figure 5.4. Summer Chinook Adult Passage Figure 5.5. Summer Chinook Jack Passage Figure 5.6. Fall Chinook Adult Passage Figure 5.7 Fall Chinook Jack Passage Figure 5.8. Coho Adult Passage Figure 5.9. Coho Jack Passage Figure Sockeye Adult Passage Figure Steelhead Adult Passage Figure Historical Annual Bonneville Dam Adult Lamprey Count Figure Historical Spring Creek National Fish Hatchery tule fall Chinook counts Figure Historical upriver bright counts at McNary Dam Figure 6.1. Hatchery release totals in Columbia River Basin (above Bonneville Dam) since Figure 6.2. Proportion of hatchery fall Chinook (tules and brights) released into each of the four river zones for out-migration in Figure 6.3. Proportion of hatchery spring Chinook released into each of the four river zones for out-migration in Figure 6.4. Proportion of hatchery coho released into each of the four river zones for outmigration in Figure 6.5. Proportion of hatchery summer and winter steelhead released into each of the four river zones for out-migration in Figure 6.6. Hatchery release totals of juvenile anadromous salmonids below Bonneville Dam since Figure 6.7. Hatchery release totals of juvenile anadromous salmonids in the Lower Columbia River Zone since Figure 6.8. Hatchery release totals of juvenile anadromous salmonids in the Mid-Columbia River Zone since Figure 6.9. Hatchery release totals of juvenile anadromous salmonids in the Snake River Zone since Draft 2013 Annual Report xii May 2014

14 List of Maps Map 5.1. Spring Chinook spatial distribution and 2013 adult dam counts as percentages of the 2012 and 10-year average counts Map 5.2. Summer Chinook spatial distributions and 2013 adult dam counts as percentages of the 2012 and 10-year average counts Map 5.3. Fall Chinook spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Map 5.4. Coho spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Map 5.5. Sockeye spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Map 5.6. Snake River Sockeye spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Map 5.7. Steelhead spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average dam counts Map 6.1 Hatchery releases of fall Chinook to the Columbia River Basin for migration year Map 6.2 Hatchery releases of spring Chinook to the Columbia River Basin for migration year Map 6.3 Hatchery releases of summer Chinook and sockeye to the Columbia River Basin for migration year Map 6.4 Hatchery releases of coho to the Columbia River Basin for migration year Map 6.5 Hatchery releases of steelhead to the Columbia River Basin for migration year Draft 2013 Annual Report xiii May 2014

15 Executive Summary To be included in the final draft. Draft 2013 Annual Report xiv May 2014

16 I. Introduction This chapter of the Fish Passage Center Annual Report was a new addition for the Annual Report in It has been added as the result of the Independent Scientific Advisory Board Scoping Review of Fish Passage Center Products (ISAB, 2010). The ISAB Review was required by the Northwest Power Conservation Council amendments to the Fish and Wildlife Program (2009). The chapter is intended to provide historical background and management context within which the Annual Report is developed for the region. The purpose of the Fish Passage Center Annual Report is to document the hydrosystem operations, environmental conditions, and the resulting fish passage characteristics that occurred during the year. In addition the report consolidates other information that is helpful in describing the year in terms of Columbia Basin salmon and steelhead passage through the hydrosystem. Reservoir operations and weather that resulted in migration flows are documented. In addition the report documents prevailing fish passage management concerns, questions, and decisions for that year by the fishery managers and hydrosystem managers. Adult returns, adult passage issues, and run size projections developed by management agencies and hatchery release data are included to complete the representation of the year. The overall objective of the Annual Report is to provide a historical reference for each year which provide a basis for future fish passage mitigation discussions and a base reference for future analysis of adult returns. A central component of the Annual Report is the Smolt Monitoring Program, which is designed to provide a long-term consistent and continuous juvenile salmon and steelhead passage characteristics data time series. The Smolt Monitoring Program data is updated daily and provided to fishery managers via the Fish Passage Center web site, to facilitate their discussions of fish passage management. This includes juvenile survival, passage timing, and passage indices by species, dissolved gas trauma monitoring, hatchery releases, and fish condition. In addition this report summarizes the environmental passage conditions, flow, spill, water temperature, project operations, studies, and research that occurred and that may have affected passage conditions. The report documents prevailing management questions or events that were discussed in the subject year. In this way the report is dynamic, reflecting the issues, analyses, decisions and discussions that occurred in that year. Many components of the report are consistent from year to year, such as the reporting of reservoir operations, adult dam counts, juvenile passage Draft 2013 Annual Report 1 May 2014

17 characteristics such as travel time, survival, passage distributions, passage timing and dissolved gas, so that year-to-year comparisons can be made. Other components of the report reflect the management issues and discussions that received focused attention in that year. These parts of the report are not consistent year to year. In recent years, new fish passage operations, such as spill for fish passage during the summer migration, raised questions and controversy regarding the benefits of these operations. In these years the Annual Report contains specific analysis addressing the benefits of spill for fish passage during the summer migration. These issues which may not be consistent from year to year are included in specific annual report because they were the focus of management debate and discussion. It provides a historical reference in which the adult and juvenile fish passage year can be understood, in the context of the conditions and events that occurred. Activities and research by others that occurred at or around the mainstem projects are briefly summarized because these activities can affect juvenile fish passage and adult passage characteristics reported for that year. In some cases the results of these activities are presented as the basis for changing or implementing different fish passage measures and passage configurations. Draft 2013 Annual Report 2 May 2014

18 II. Water Supply A. Water Supply Water Year (WY) 2013 appeared near average early in the winter throughout most of the Columbia basin. However, by late spring, runoff fell below average in the Snake Basins, but remained average or above in the middle and upper Columbia. At The Dalles Dam, the observed runoff recorded between January and July of 2013 was Maf, which was 96% of the average runoff between 1981 and (Table 2.1). Runoff at other Columbia River Basin locations ranged between 87% and 122% of average. At Lower Granite Dam the observed runoff recorded between April and August of 2013 was Maf, which was 70% of the average runoff between 1981 and 2010 (Table 2.1). Over the 85-year record between 1929 and 2013, the 2013 January July runoff at Lower Granite Dam and The Dalles Dam ranked 70th and 50th, respectively (Table 2.2). Table 2.1. January and March Final Water Supply Forecasts and observed runoff at The Dalles, Grand Coulee, Lower Granite, Libby, Dworshak, and Hungry Horse dams over various time periods in WY Site January Final Water Supply Forecast (Maf) March Final Water Supply Forecast 2 (Maf) Observed Runoff (Maf) The Dalles (Jan July) Grand Coulee (Jan July) Lower Granite Res. Inflow (Apr Aug) Libby Res. Inflow, MT (Apr Aug)* Dworshak Res. Inflow (Apr July)* Hungry Horse Res. Inflow, MT (Jan July)** Note: Unless otherwise noted, forecasts from Northwest River Forecast Center. *Indicates COE issued final forecast **Indicates Bureau of Reclamation final forecast Obs. Percent of Average (%) Water Supply, snowpack, and precipitation are expressed as a percent of normal, which is currently the average of a particular variable over the period. The significance of the normal period can be found at: Draft 2013 Annual Report 3 May 2014

19 Table 2.2 Observed Runoff at Lower Granite Dam and The Dalles Dam from January July 2 from 1991 to 2013 along with each year s rank in terms of the 85-year record between 1929 and 2013 (lower rank = higher water year). Lower Granite (Jan-July) The Dalles (Jan-July) Year Runoff (Maf) Rank Runoff (Maf) Rank Precipitation was generally near average over WY For WY 2013 (October 2012 through September 2013) precipitation was (1) 100 percent of average ( ) at the Columbia River above Grand Coulee Dam, (2) 80 percent of average at the Snake River above Ice Harbor Dam, and (3) 90 percent of average at the Columbia River above The Dalles Dam. Table 2.3 displays precipitation by month and over WY 2013 at the Columbia River above Grand Coulee Dam, the Snake River above Ice Harbor Dam, and at the Columbia River above The Dalles Dam. The three sites shown in Table 2.3 encompass large portions of the Columbia and Snake River basins. In general, the heaviest monthly precipitation (with respect to average) occurred at the beginning and end of WY 2013 in October of 2012 and September of There are several time periods in which water supply forecasts and observed runoff are calculated. The January through July period is useful as it incorporates the winter period as well as the entire spring period and a portion of the summer period. January to July runoff volumes at The Dalles and Lower Granite are available back to Draft 2013 Annual Report 4 May 2014

20 The month of June recorded variable precipitation; the Columbia above Grand Coulee contained 124% of average precipitation while the Snake above Ice Harbor Dam was only 61% of average (March and April followed a similar trend). Table 2.3 Individual month and Water Year 2013 precipitation from October 1, 2012, to September 30, 2013, at select locations within the Columbia Basin in percent of normal ( ). Month Columbia above Grand Coulee Dam Snake River above Ice Harbor Dam Columbia above The Dalles Dam October % 130% 164% November % 97% 102% December % 108% 94% January % 52% 49% February % 47% 50% March % 54% 72% April % 64% 87% May % 55% 82% June % 61% 98% July % 31% 21% August % 51% 75% September % 248% 225% Water Year 2013 Oct 2012 Sept % 80% 90% Note: Data can be found at Snowpack throughout the Columbia Basin varied in In basins above the Snake River confluence, snowpack generally increased with respect to average through the end of April. However, in Snake River basins and Lower Columbia basins snowpack decreased with respect to average through the end of April. By the 1st of March, most basins contained at, or near average, snowpack for that same time of year. By the end of April, snowpack was: 101% of average in Columbia River Basins above the Snake River confluence, 75% of average in Snake River Basins, and 77% of average in Lower Columbia River Basins between Bonneville Dam and McNary Dam (Table 2.4). By mid-may, Columbia River Basin snowpack was: 75% of average in Columbia River Basins above the Snake River confluence, 46% of average in Snake River Basins, and 37% of average in Lower Columbia River Basins between Bonneville Dam and McNary Dam (Table 2.4). Draft 2013 Annual Report 5 May 2014

21 Table 2.4 Seasonal snow water equivalents at select basins during various points of Water Year 2013 Data from ftp://ftp.wcc.nrcs.usda.gov/data/snow/update/columbia/. March 1, 2013 Snow Water Equivalent (% Avg.) March 31, 2013 Snow Water Equivalent (% Avg.) April 30, 2013 Snow Water Equivalent (% Avg.) May 15, 2013 Snow Water Equivalent (% Avg.) Basin Columbia River above the Snake River Confluence Kootenai River in Montana Flathead River Upper Clark Fork River Bitterroot Lower Clark Fork River Idaho Panhandle Region Columbia above Methow Chelan, Entiat, Wenatchee Yakima, Ahtanum Average * Snake River Snake River above Palisades Henry Fork, Teton, Willow, Blackfoot, Portneuf Big and Little Wood Big and Little Lost Raft, Goose, Salmon Falls, Bruneau Weiser, Payette, Boise Rivers Owyhee Malheur Grande Ronde, Powder, Burnt, Imnaha Rivers Clearwater and Salmon Rivers Average * Lower Columbia between Bonneville and McNary Umatilla, Walla Walla Rivers, Willow Creek Deschutes, Crooked, John Day Rivers Lower Columbia, Hood River Average * * The averages presented in the table above are straight averages; they are not weighted by area. B. Water Supply/Management Impacts to Biological Opinion Measures 1. Grand Coulee Dam Figure 2.1 illustrates the operation of Grand Coulee Dam throughout the winter/spring with respect to flood control. Grand Coulee Dam was primarily operated to its flood control elevations over the winter period (Figure 2.1). Over the early winter of 2013 Grand Coulee Dam was drafted to meet power needs and chum tailwater elevations below Bonneville Dam. Grand Draft 2013 Annual Report 6 May 2014

22 Coulee Dam ended April 10 th at an elevation of feet, 2.9 feet below its April 10 th Flood Control (FC) 3 target elevation of ft (Figure 2.1, Table 2.5). Being at or near the April 10 th Biological Opinion (BiOp) FC Elevations is intended to position a particular project at its highest possible elevation (within the constraints of flood control) on April 10 th, causing the least amount of refill during the Spring Flow Objective periods. The refill of Grand Coulee is triggered one day before the date that the forecasted unregulated flow at The Dalles is expected to exceed the Initial Controlled Flow (ICF). 4 In 2013, the ICF calculated in April was Kcfs; this flow was met at The Dalles on May 10, Reservoir Elevation Actual Reservoir Elevation Full Pool Reservoir Elevation January FC Elevations February FC Elevations March FC Eelvations March Shifted FC April 10th Shifted FC April 30th FC Time Figure 2.1 Operations at Grand Coulee Dam over WY The Action Agencies calculate Flood Control Elevations based on Final Water Supply Forecasts. The April 10 th BiOp Flood Control elevations are linearly interpolated between the March 31 and April 15 Flood Control Elevations calculated using the March Final Water Supply Forecast. 4 The Initial Controlled Flow is a storage reservoir refill trigger. Refill begins on the date that the forecasted unregulated flow at The Dalles reaches a computed flow called the Initial Controlled Flow. Draft 2013 Annual Report 7 May 2014

23 Table 2.5. April 10 th Biological Opinion Flood Control Elevations at Grand Coulee, Libby, Dworshak, Hungry Horse, and Brownlee along with actual elevations on April 10, April 10 th BiOp FC Elevation* (feet) Actual April 10 th Elevation (feet) Difference between April 10 th BiOp FC and Actual April 10 th Elevation (ft) Dam Grand Coulee Libby Dworshak Hungry Horse Brownlee * April 10 th BiOp Elevations were linearly interpolated between the April 1 st and April 15 th flood control elevations issued in March Grand Coulee Dam reached its peak elevation of feet on July 12, The peak elevation at Grand Coulee Dam in 2013 was slightly less than the full elevation (1290 feet) as requested by the Fish Flow Releases Advisory Group (FFRAG) to demonstrate that a portion of the Lake Roosevelt (Grand Coulee) Incremental Storage Release Program water was released over the spring period. In 2013, the end of August BiOp draft limit at Grand Coulee Dam was 1278 feet. The BiOp end of August draft elevation at Grand Coulee Dam is dependent on the July Final Water Supply Forecast (April August) at The Dalles Dam. When the July Final forecast at The Dalles Dam equals or exceeds 92 Maf, the end of August draft elevation at Grand Coulee Dam is 1280 feet. When this forecast is below 92 Maf, the end of August draft limit is 1278 feet. In 2013, the July final forecast (April August) at The Dalles Dam was 88.6 Kaf. The 2013 end of August draft was further lowered by the Lake Roosevelt (Grand Coulee) Incremental Storage Release Program which requested that the end of August elevation at Grand Coulee be lowered an additional 0.6 feet (relative to the 1278 ft BiOp draft elevation). On August 31, 2013, at midnight, Grand Coulee Dam was at an elevation of feet. In total, 25.5 Kaf of water was released as part Lake Roosevelt Incremental Storage in Dworshak Dam Figure 2.2 displays the operation of the Dworshak Dam throughout the winter/spring with respect to flood control. Dworshak was operated near Flood Control Elevations throughout the late winter and early spring period of WY On April 10th, Dworshak was at an elevation of feet, 5.1 feet above its April 10th FC target elevation of ft (Figure 2.2, Table 2.5). Being at or near the April 10th BiOp FC Elevations is intended to position a particular project at its highest possible elevation (within the constraints of flood control) on April 10th, causing the least amount of refill during the Spring Flow Objective periods. In 2013, Dworshak reached a minimum elevation of feet on January 23, 2013, after which time the project steadily refilled. Draft 2013 Annual Report 8 May 2014

24 Dworshak Dam reached a peak elevation of feet (full) on June 16, 2013, however it was within one foot of full over most of June (June 6 30). Over the summer months Dworshak Dam was drafted to elevation feet on August 31, 2013, for flow augmentation and temperature regulation in the lower Snake River, leaving slightly less than 200 Kaf of Dworshak water to be released over the first portion of September. Dworshak Dam reached elevation 1520 feet on September 21, Reservoir Elevation Actual Reservoir Elevation Full Pool Reservoir Elevation January FC Elevations (system) February FC Elevations (System) March FC Elevations (System) April 10th FC Time Figure 2.2. Operations at Dworshak Dam over WY Libby Dam In Water Year 2013, the December COE forecast at Libby for the April August period was 6238 Kaf, which resulted in the project planning to draft to the full end of December FC elevation of 2411 feet by the end of December. The current criteria that determines the end of December Draft at Libby Dam is based on the USACE December (April August) forecast. The criteria for determining the end of December draft is as follows: Draft 2013 Annual Report 9 May 2014

25 Relax FC 600 KAF if COE forecast is < 5500 KAF No FC Relaxation if COE forecast is > 5900 KAF Between 5500 KAF and 5900 KAF, interpolate to determine FC relaxation volume. By December 31 st of 2012, the USACE drafted Libby to an elevation of feet, slightly below the end of December FC Elevation of 2411 feet (Figure 2.3) Reservoir Elevation Actual Reservoir Elevation Full Pool Reservoir Elevation January FC Elevations February FC Elevations March FC Elevations April 10th FC Elevation April 30 FC Time Figure 2.3. Operations at Libby Dam over WY Libby Dam was operated to flood control in January but by February, March, and April the reservoir elevation of Libby Dam fell below flood control despite reducing outflows to the 4 Kcfs minimum early in February. By April 10 th, Libby Dam was at an elevation of feet, 7.4 feet below its April 10 th FC elevation (Figure 2.3 and Table 2.5). On May 8, 2013, the U.S. Fish and Wildlife Service (USFWS) submitted System Operational Request (SOR) FWS to the Action Agencies that requested a Tier 3 Sturgeon Draft 2013 Annual Report 10 May 2014

26 Pulse Operation 5 in 2013 at Libby Dam ( At the May 8, 2013, TMT meeting this SOR was discussed and the Action Agencies agreed to implement the SOR as written. The sturgeon pulse occurred between May 11 th and June 10 th, with releases of 1.19 Maf above the 4 Kcfs minimum outflow at Libby Dam. On April 3, 2013, the Kootenai Tribe of Idaho submitted SOR to the Action Agencies that requested minimal flows of 8 Kcfs in September and October for Phase 2 of the Kootenai River Habitat Restoration Project. After the high June precipitation and inflows at Libby Dam, SOR was re-discussed at TMT through July and August. The implementation of SOR was modified to outflows of 6 Kcfs for most of September and 4 Kcfs in October. Libby Dam reached a peak elevation of feet (2459 feet is full) on July 6, Libby Dam drafted to elevation feet by the end of September. The 2013 Water Management plan states that during July and August, Libby Dam was to be drafted 10 ft from full (2449 ft) by the end of September to help meet the flow objectives for juvenile salmon in the Columbia River (except in lowest 20 th percentilewater years The Dalles April August <72.2 Maf when draft will increase to 20 ft from full by the end of September). 4. Hungry Horse Dam Throughout much of the late winter and early spring, Hungry Horse Dam was operated near flood control elevations (Figure 2.4) and was operating to meet Columbia Falls minimum flows. On April 10 th, Hungry Horse was at an elevation of feet, 0.6 feet above its April 10 th Flood Control Elevation of feet (Figure 2.4, Table 2.5). Beyond April 10 th, Hungry Horse drafted slightly until reaching a minimum elevation of 3526 feet on May 5, 2013, then began to refill on May 6, Hungry Horse reached a peak elevation of feet on July 8, 2013, slightly below full (3560 feet). The 2013 Water Management plan states that the summer draft limit at Hungry Horse is 3550 feet (10 feet from full) by the end of September except in the lowest 20 th percentile water years (The Dalles April August <72.2 Maf), when the draft limit will be 3540 feet (20 feet from 5 The Sturgeon Pulse Operation refers to water released at Libby Dam for a spring sturgeon flow pulse during the May through July period intended to provide water for sturgeon spawning and egg incubation. Draft 2013 Annual Report 11 May 2014

27 full) by end of September. Hungry Horse Dam drafted to elevation feet by the end of September Reservoir Elevation Actual Reservoir Elevation Full Pool Reservoir Elevation January FC Elevations February FC Elevations March FC Elevations April 10th FC April 30th FC Time Figure 2.4. Operations at Hungry Horse Dam over WY Brownlee Dam Brownlee Dam began the Water Year at an elevation of feet. On April 10 th, Brownlee Dam was at an elevation of feet, 8.7 feet below its flood control elevation of feet (Table 2.5). Brownlee continued to draft through May 4, 2013, after which refill was initiated. Brownlee Dam reached its peak elevation of feet on June 19, 2013 (Figure 2.5). Draft 2013 Annual Report 12 May 2014

28 Reservoir Elevation Actual Reservoir Elevation Full Pool Reservoir Elevation January FC Elevations February FC Elevations March FC Elevations April 10th FC April 30th FC Time Figure 2.5. Operations at Brownlee Dam over WY C. Spring/Summer Flow Objectives The following table summarizes the spring 6 and summer BiOp flow objectives and actual flows for 2013 at Lower Granite, Priest Rapids, and McNary dams. Bold font indicates that the spring or summer actual average flow was equal to or greater than the flow objective. 6 Spring Flow Objectives are in place at McNary Dam, Priest Rapids Dam, and Lower Granite Dam. With the exception of Priest Rapids Dam, flow objectives at McNary and Lower Granite are variable and depend on April Final Water Supply Forecasts. The spring flow objective at Priest Rapids is 135 Kcfs (April 10 June 30) in all years. The McNary Flow objective (April 10 June 30) varies between 220 and 260 Kcfs dependent upon on the April Final Water Supply forecast at The Dalles Dam (April to August period). And the Lower Granite Flow Objective ranges between 85 and 100 Kcfs and is dependent upon the April Final Water Supply Forecast at Lower Granite (April to July period). Draft 2013 Annual Report 13 May 2014

29 Table 2.6. Spring and summer flow averages at Lower Granite, McNary, and Priest Rapids dams during their respective spring and summer Biological Opinion periods Dam Spring Flow Objective Spring Average Summer Flow Objective Summer Average Lower Granite Dam McNary Dam Priest Rapids Dam N/A N/A Note: There is not a summer flow objective period at Priest Rapids Dam. Bold Font indicates Flow Objective met. Overall, taking into account all of the projects with BiOp flow objectives (all blocks in the above table), 2013 BiOp seasonal flow objectives were met only over the spring periods at McNary and Priest Rapids Dams (Table 2.6). Table 2.7 displays weekly average flows at Lower Granite, McNary, and Priest Rapids dams over the spring and summer period. Figures 2.6, 2.7, and 2.8 display daily flows and flow objectives at Lower Granite, McNary, and Priest Rapids dams over the spring and summer periods. Table 2.7. Spring and summer weekly flow averages at Lower Granite, McNary, and Priest Rapids dams during the 2013 spring and summer Biological Opinion periods. Average flow at Average flow at Average flow at Week Lower Granite (Kcfs) McNary (Kcfs) Priest Rapids (Kcfs) April April April April May May May May May 29-June June June June June 26-July July July July July July 31-August August August August August Note: There is not a summer flow objective period at Priest Rapids Dam. See Table 2.6 for spring and summer flow objectives. Draft 2013 Annual Report 14 May 2014

30 River flows in the lower Columbia River at McNary Dam were moderately high early in the flow objective period (above flow objective) followed by a slight decrease for several weeks before sharply increasing to a peak on May 11, 2013, of Kcfs. Flows gradually receded to slightly below the flow objective by mid-june. Figure 2.6 displays the shape of the runoff over the spring and summer at McNary Dam along with the spring and summer flow objectives Actual Discharge BiOp Objective 300 Discharge (Kcfs) Spring Average Flow = Kcfs Spring BiOP Objective = 226 Kcfs Summer Average Flow = Kcfs Summer BiOp Objective = 200 Kcfs Apr-13 2-May May Jun Jul-13 2-Aug Aug-13 Date Figure 2.6. Spring and summer Biological Opinion flow objectives and actual flows at McNary Dam over the BiOp period. The shape of the flow in the lower Snake River at Lower Granite Dam was similar to McNary, however early April flows did not rise above the spring flow objective of 85 Kcfs. Flows at Lower Granite did demonstrate an early peak (75.8 Kcfs) followed by a decrease in flow for a period of approximately one month before exceeding the spring flow objective on May 7, Lower granite flows peaked on May 11, 2013, at Kcfs, but remained above the spring flow objective only for a period of 11 days. Beyond the spring peak, flows at Lower Granite receded quickly and exceeded the summer flow objective (50 Kcfs) only for one day of the summer flow period. The summer flow average at Lower Granite Dam was the second lowest since 1995 (2001 was lower), with flows falling below 20 Kcfs for 5 days in middle to Draft 2013 Annual Report 15 May 2014

31 late August. Figure 2.7 displays the shape of the runoff over the spring and summer at Lower Granite Dam along with the spring and summer flow objectives Actual Discharge BiOp Objective 120 Discharge (Kcfs) Spring Average Flow = 67.9 Kcfs Spring BiOp Objective = 85 Kcfs Summer Average Flow = 29.9 Kcfs Summer BiOp Objective = 50 Kcfs Apr-13 3-May-13 2-Jun-13 2-Jul-13 1-Aug Aug-13 Date Figure 2.7. Spring and summer Biological Opinion flow objectives and actual flows at Lower Granite Dam over the BiOp period. Flows at Priest Rapids Dam were above the 135 Kcfs spring flow objective for the entire spring period of April 10 June 30. Priest Rapids flows began the spring period near 200 Kcfs for approximately one week before decreasing slightly to near 150 Kcfs through the first week of May. By early in the second week of May, flows at Priest Rapids again exceeded 200 Kcfs and remained above this level through most of May. Flows at Priest Rapids Dam again increased in mid-june, reaching a peak discharge on June 30, 2013, of Kcfs. Figure 2.8 displays the shape of the runoff over the spring at Priest Rapids Dam. Draft 2013 Annual Report 16 May 2014

32 Actual Discharge BiOp Objective 200 Discharge (Kcfs) Spring Average Flow = Kcfs Spring BiOP Objective = 135 Kcfs Apr Apr May-13 8-Jun Jun-13 Date Figure 2.8. Spring Biological Opinion flow objectives and actual flows at Priest Rapids Dam over the BiOp period. D. Dworshak Dam Summer Operations for Temperature Regulation at Lower Granite Dam The Dworshak reservoir is used for flow augmentation and for temperature regulation at Lower Granite Dam during the summer fish migration. Water temperatures in the Lower Granite tailwater exceeded the temperature standard (20 C) for 116 hours between July 1 and September 30, Figure 2.9 displays tailwater temperatures and the temperature standard at Lower Granite Dam as well as the temperature and magnitude of discharges from Dworshak Dam. 7 7 Lower Granite and Dworshak data obtained from: Draft 2013 Annual Report 17 May 2014

33 25 20 Temperature (deg C) Lower Granite Tailwater Temperature Dworshak Release Temperature Temperature Standard Dworshak Outflow Discharge Dworshak Outflow Discharge (Kcfs) 0 0 July 1, 2013 July 8, 2013 July 15, 2013 July 22, 2013 July 29, 2013 August 5, 2013 August 12, 2013 August 19, 2013 Date August 26, 2013 September 2, 2013 September 9, 2013 September 16, 2013 September 23, 2013 September 30, 2013 Figure 2.9. Tailwater temperature and temperature standard at Lower Granite Dam as well as the temperature and magnitude of discharges from Dworshak Dam from July 1 to September 30, The Salmon Managers and Action Agencies discussed Dworshak Dam water releases and the resultant impact on Lower Granite Dam temperatures during each TMT meeting that took place in July and August of Dworshak Dam releases were at or above full powerhouse capacity (approximately Kcfs) from July 1 through August 12, 2013, and ranged between 7.4 and 8.6 Kcfs from August 13 through September 8, 2013 (Figure 2.9). As part of the Snake River Adjudication, 200 Kaf of flow augmentation from Dworshak Dam is provided for late summer flow augmentation in the lower Snake River (beyond the August 31 st date prescribed in the BiOp to at least September 15 th ). It is intended that this water will help juvenile salmon remaining in the river migrate downstream and also help adult salmonids still migrating upstream. On August 31, 2013, Dworshak Dam was at an elevation of feet, leaving slightly less than 200 Kaf of flow augmentation for the first portion of September. Dworshak Dam drafted to elevation 1520 feet on September 21, Draft 2013 Annual Report 18 May 2014

34 E. Canadian Operations 8 Waiting on Info. F. Snake River Low runoff conditions in the Boise (50% of average), Payette (62%), and the Snake River above Milner (70%) did not allow for the target release of 487,000 acre-feet of flow augmentation water above Brownlee Dam, as identified in the 2005 Upper Snake BiOp. The Bureau of Reclamation (BOR) was able to release 427,000 acre-feet for flow augmentation in 2013 from the Upper Snake above Milner (154,885 acre-ft), the Payette (175,621 acre-ft), the Boise (18,845 acre-ft), and natural flows (77,649 acre-ft). G. Summary The observed runoff at The Dalles Dam between January and July of 2013 was Maf (96% of average). The observed runoff at Lower Granite Dam between April and August of 2013 was Maf (70% of average). Water Year 2013 (October 2012 through September 2013) precipitation was 100% of the average at the Columbia River above Grand Coulee Dam, 80% of average at the Snake River above Ice Harbor Dam, and 90% of average at the Columbia River above The Dalles Dam. By the end of April, Columbia River Basin snowpack was 101% of average in Columbia River Basins above the Snake River confluence, 75% of average in Snake River Basins, and 77% of average in Lower Columbia River Basins between Bonneville Dam and McNary Dam. Grand Coulee Dam ended April 10 th at an elevation of feet, 2.9 feet below its April 10 th FC target elevation of feet. Grand Coulee Dam reached its peak elevation of feet on July 12, The BiOp end of August draft limit was 1278 feet and lowered an additional 0.6 feet for the Lake Roosevelt (Grand Coulee) Incremental Storage Release Program. At midnight on August 31, 2013, Grand Coulee Dam was at an elevation of feet. In total, 25.5 Kaf of water was released as part Lake Roosevelt Incremental Storage in On April 10 th, Dworshak was at an elevation of feet, 5.1 feet above its April 10 th FC target elevation of ft. Dworshak Dam reached a peak elevation of feet (full) on June 16, 2013, and was drafted to elevation feet on August 31 st, 2013, for flow augmentation and temperature regulation in the lower Snake River, 8 Information in the Canadian Operations section was obtained from The Bonneville Power Administration. Draft 2013 Annual Report 19 May 2014

35 leaving slightly less than 200 Kaf of Dworshak water to be released over the first portion of September. Dworshak Dam reached elevation 1520 feet on September 21, By December 31 st of 2012, the USACE drafted Libby to an elevation of feet, slightly below the end of December FC Elevation of 2411 feet. On April 10 th, Libby Dam was at an elevation of feet, 7.4 feet below its April 10 th FC elevation. On May 8, 2013, the USFWS submitted SOR FWS that requested a Tier 3 Sturgeon Pulse Operation. The sturgeon pulse occurred between May 11 th and June 10 th, with releases of 1.19 Maf above the 4 Kcfs minimum outflow at Libby Dam. On April 3, 2013, the Kootenai Tribe of Idaho submitted SOR to the Action Agencies that requested minimal flows of 8 Kcfs in September and October for Phase 2 of the Kootenai River Habitat Restoration Project. The implementation of SOR was modified to outflows of 6 Kcfs for most of September and 4 Kcfs in October. Libby Dam reached a peak elevation of feet (2459 feet is full) on July 6, 2013, and drafted to elevation feet by the end of September. On April 10 th, Hungry Horse was at an elevation of feet, 0.6 feet above its April 10 th FC Elevation of feet. Hungry Horse reached a peak elevation of feet on July 8, 2013, and drafted to elevation feet by the end of September. On April 10 th, Brownlee Dam was at an elevation of feet, 8.7 feet below its flood control elevation of feet. Brownlee Dam reached its peak elevation of feet on June 19, Biological Opinion seasonal flow objectives were met only over the spring periods at McNary and Priest Rapids dams. River flows in the lower Columbia River at McNary Dam were moderately high early in the flow objective period (above flow objective) followed by a slight decrease for several weeks before sharply increasing to a peak on May 11, 2013, of Kcfs. Lower Granite flows peaked on May 11, 2013, at Kcfs, but remained above the spring flow objective only for a period of 11 days. Beyond the spring peak, flows at Lower Granite receded quickly and exceeded the summer flow objective (50 Kcfs) for only one day of the summer flow period. The summer flow average at Lower Granite Dam was the second lowest since 1995 (2001 was lower), with flows falling below 20 Kcfs for 5 days in middle to late August. Flows at Priest Rapids Dam were above the 135 Kcfs spring flow objective for the entire spring period of April 10 June 30. Water temperatures in the Lower Granite tailwater exceeded the temperature standard (20 C) for 116 hours between July 1 and September 30, Dworshak Dam releases were at or above full powerhouse capacity (approximately Kcfs) from July 1 through August 12, 2013, and ranged between 7.4 and 8.6 Kcfs from August 13 through September 8, On August 31, 2013, Dworshak Dam was Draft 2013 Annual Report 20 May 2014

36 at an elevation of feet, leaving slightly less than 200 Kaf of flow augmentation for the first portion of September. Dworshak Dam drafted to elevation 1520 feet on September 21, The BOR was able to release 427,000 acre-ft for flow augmentation in 2013 from the Upper Snake above Milner (154,885 acre-ft), the Payette (175,621 acre-ft), the Boise (18,845 acre-ft), and natural flows (77,649 acre-ft). Draft 2013 Annual Report 21 May 2014

37 III Spill Management A. Spill 1. Overview The purpose of providing a spill program is to improve the downstream passage survival of juvenile salmonid stocks by providing a route associated with reduced project passage delay and with less direct and delayed mortality relative to powerhouse bypass or turbine passage. Spill is also used to provide an alternate route for fish at transportation collector projects, allowing an increased proportion of juvenile salmonids to migrate in-river to below Bonneville Dam. Presently, this "spread the risk" management option is employed since transportation does not provide the survival to adulthood needed for population recovery (Tuomikoski et al., 2013) for ESA listed spring/summer Chinook, steelhead, sockeye and fall Chinook. The Comparative Survival Study (CSS) has conducted analyses comparing the survival of fish that pass a hydroelectric project undetected at a transportation collection site (C0) in the Snake River versus fish that have passed through a bypass (C1). The smolt-to-adult return rates (SARs) indicate that bypassed juvenile Chinook and steelhead appear to have a lower SAR than undetected in-river migrants that did not pass through the powerhouse juvenile bypass system, with the magnitude of those differences varying across years (Tuomikoski et al., 2009, 2010, 2011, 2012, 2013). The addition of the most recent data to the historic CSS time series continues to show the importance of spill and flow for in-river juvenile survival and SARs (Haeseker et al., 2012). Additionally, recent analytical results of salmon life-cycle survival modeling indicate that spillway passage affects survival throughout the life cycle. Chinook adult returns declined with multiple passages through powerhouses at dams (Petrosky and Schaller, 2010, Schaller et al., 2014). Analyses conducted by NOAA Fisheries in the development of the Biological Opinions showed that smolt-to-adult return rates for Chinook and steelhead were related to arrival time at Bonneville Dam, and that multiple bypass passage reduced SARs (Scheurell and Zabel, 2007). Juvenile fish travel time was consistently fastest when water transit time (WTT) is reduced (i.e., higher water velocity) and spill levels are high. The effect of spill most likely influences the amount of time required to migrate through the forebay, concrete and tailrace areas of the dams themselves. In the case of steelhead and subyearling Chinook, there is evidence that as the number of dams with surface passage structures has increased, fish travel times have declined, but there was less evidence of this for yearling Chinook. The instantaneous mortality rates tend to be lowest under conditions of fast WTT and high spill levels. In addition, mortality rates tend Draft 2013 Annual Report 22 May 2014

38 to increase over the migration season. There was also some evidence that the increased number of dams with surface passage structures in the spillways may be reducing mortality rates. These analyses continue to suggest that there is opportunity to reduce fish travel time and increase survival throughout the Federal Columbia River Power System (FCRPS) through increases in spill levels up to the tailrace dissolved gas limits (Tuomikoski et al., 2012). Spilling water over a hydroelectric project, under some conditions can generate atmospheric gas supersaturation of the river that may have detrimental effects on fish. In providing spill as an alternate passage route, the associated potential for mortality due to dissolved gas supersaturation is balanced against mortality of turbine passage and the long-term benefits of spill passage, including: a reduction in juvenile travel time; an increase in reach survival; and an avoidance of bypass passage and higher smolt-to-adult return rates. If the total dissolved gas due to voluntary spill for fish passage exceeds the states criteria, actions are required to reduce the total dissolved gas (TDG). These actions can include changing the spill pattern or reducing the total amount of spill. However, monitoring migrating populations for signs of gas bubble trauma since 1994 has shown that problematic dissolved gas levels have not occurred with the provision of voluntary planned levels of spill for fish passage. Problematic total dissolved gas levels usually are observed when spill exceeds voluntary spill levels and uncontrolled spill, due to flows in excess of hydraulic capacity or generation needs, occurs. At that point there are no measures or actions that can be taken to decrease TDG in the hydrosystem. 2. Spill Planning and Operations On March 28, 2013, the COE s Fish Operations Plan (FOP; USACE, 2013) for spring and summer of 2013 operations was approved by the U.S. District Court of Oregon. The FOP specified the same fish operations that occurred in 2012 for 2013, subject to modifications necessary to accommodate new structures and research at specific dams. Spill, according to the 2013 spring and summer FOP, occurs in all flow years. Spill was a court ordered rollover of 2012 operations with the federal parties interpreting this to mean providing spill at Ice Harbor Dam exactly as was provided in the 2012 FOP, which was an operation that mimicked what would have occurred if a study was conducted, even though a study has not been conducted at this project since It also includes using the Camas/ Washougal TDG monitor as a point of compliance for measuring TDG below Bonneville Dam even though it was not a required point of compliance by the Oregon Department of Environmental Quality or Washington Department of Ecology in The use of the Camas/ Draft 2013 Annual Report 23 May 2014

39 Washougal monitor has the effect of limiting spill at Bonneville Dam when the TDG at this monitor exceeds 115%, even though the Water Quality Agencies do not require its use. Plan. The following table describes the planned spill levels according to the 2013 Fish Operations Table 3.1. Planned spill levels for the FCRPS during spring and summer Season/Project Spring Lower Granite Little Goose Lower Monumental Ice Harbor McNary John Day The Dalles Bonneville Summer Lower Granite Little Goose Lower Monumental Ice Harbor McNary John Day The Dalles Bonneville 2013 Agreement Spill Levels 20 Kcfs instantaneously 30% of instantaneous flow Gas Cap* levels instantaneously April 3 April 28: 45 Kcfs during the day/gas Cap during the night April 29 June 20: 30% of instantaneous flow vs. 45 Kcfs during the day/gas Cap during the night 40% of instantaneous flow Pre-test: 30% of instantaneous flow; Testing: 30% of instantaneous flow vs.40% of instantaneous flow 40% of instantaneous flow 100 Kcfs instantaneously 18 Kcfs instantaneously 30% of instantaneous flow 17 Kcfs instantaneously June 21 July 13: 30% of instantaneous flow vs. 45 Kcfs during the day /Gas Cap during the night July 13 August 31: 45 Kcfs/Gas Cap during the night 50% of instantaneous flow Testing (July 1 July 20): 30% of instantaneous flow vs. 40% of instantaneous flow Post-Test (July 21 August 31): 30% of instantaneous flow 40% of instantaneous flow Testing (June 16 July 20): 85 Kcfs during the day/121 Kcfs during the night vs. 95 Kcfs instantaneously Post-Testing (July 21 August 31): 75 Kcfs during the day/gas Cap during the night Note: In the Snake River spring spill occurs from April 3 through June 20 and summer spill occurs from June 21 through August 30. The spring spill period in the middle Columbia River is from April 10 through June 30 and the summer spill season is from July 1 through August 30. * Gas cap is defined as the volume of spill that does not exceed the standards of 120% total dissolved gas in the tailrace of a specific project and, where applicable, the 115% total dissolved gas level in the next downstream forebay from a project. January July runoff in 2013 was 70% of average ( ) above Lower Granite and 97% of average above The Dalles Dam. The runoff (January July) volume for the 2013 water year was near average in the Lower Columbia River but below average in the Lower Snake River. Runoff (January July) was 96% of average ( ) at The Dalles Dam and 69% of average at Lower Granite Dam. In the Snake River, this resulted in mostly lower than average flows throughout the spring and summer seasons, with peak flows in May (Figure L-1). In the Lower Columbia, the 2013 runoff resulted in near average flows in both the spring and summer Draft 2013 Annual Report 24 May 2014

40 periods (Figure L-2). The peak flow conditions in the Snake River and Lower Columbia rivers in mid-may resulted in uncontrolled spill for a few days at the Snake and Columbia River sites. Spill during 2013 generally met the objectives of the 2013 FOP, within the constraints of research study requirements, managing to the dissolved gas criteria of 120% TDG in the tailraces of the dams and 115% in the forebays of the dams, and the requirements for minimum turbine operations at each project. 3. Project-Specific Operations a) Snake River Prior to the implementation of fish spill in the Snake River on April 3 rd, the spill that occurred was due to high flows, unit outages, and the necessary drafting of reservoirs to meet flood control elevations. Dworshak Dam Very little spill occurred throughout April through June (Figure 3.1). Spill occurred though at some times during July as water was released from Dworshak for summer flow augmentation and temperature control in the lower Snake River. Figure 3.1. Dworshak (DR) Dam flow and spill for spring and summer of Lower Granite Dam Spring spill occurred from April 3 through June 20 and summer spill occurred from June 21 to August 31 (Figure 3.2). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure 3.3. The 2013 FOP specified that the project spill 20 Kcfs on an instantaneous basis during the spring period and an instantaneous 18 Kcfs during the summer spill period (RSW operation plus training spill). Draft 2013 Annual Report 25 May 2014

41 Figure 3.2. Lower Granite Dam (LGR) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure 3.3. Historic spill at Lower Granite Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. In early May spill levels were decreased in response to TDG levels measured in the Little Goose Dam forebay, but as flows increased later in May, spill met or exceeded the 20 Kcfs spill Draft 2013 Annual Report 26 May 2014

42 level described in the 2013 FOP. Throughout the summer period the Lower Granite Dam spill was a combination of (1) spill meeting the 2013 FOP volume, (2) being below the 2013 FOP volumes due to low flow and powerhouse minimum requirements, (3) being below the 2013 FOP volumes due to special operations to address adult sockeye passage, and (4) exceeding the 2013 FOP volumes as a result of acoustic Doppler current profile surveys to obtain water velocities to calibrate the COE s model for the future construction of the juvenile bypass outfall, and roof repairs. In late July adult sockeye passage issues precipitated changes in operation including the prioritization of the operation of Unit 1, which requires a higher flow (16.9 Kcfs) to operate at the 1% efficiency range due to its fixed blade configuration. The 24 hour operation of Unit 1 was implemented from July 29th until the evening of August 5th when mounting concern regarding decreased juvenile protection, and limited adult passage improvement, resulted in a change in operations. The revised operation, which lasted until August 10 th, was for the daytime (0500 to 1700 hours) operation of Unit 1, and the provision of spill in excess of that required for station service during nighttime hours (1700 to 0500 hours). After August 10th Lower Granite Dam spill was greater than the Court ordered spill levels as a result of limiting daytime operation to station service (5 Kcfs) to allow repairs to the powerhouse roof. Little Goose Dam Spill according to the 2013 FOP was 30% of instantaneous flow throughout the spring and summer period. Spill levels of 30% were generally met or exceeded during the spring period (Figure 3.4). Figure 3.4. Little Goose Dam (LGS) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Draft 2013 Annual Report 27 May 2014

43 During the summer spill period, spill met or exceeded the 30% of instantaneous flow through early August. Low flows initiated a change in spill from the 30% of instantaneous flow to a constant spill level in the 7 11 Kcfs range. This change was initiated on the afternoon of July 18 th. The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure 3.5. Figure 3.5. Historic spill at Little Goose Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. Lower Monumental Dam According to the 2013 FOP, spill at Lower Monumental Dam was planned to the gas cap throughout the spring period and 17 Kcfs throughout the summer period. During most of May the COE kept re-establishing spill caps to manage to the 115% TDG in the Ice Harbor forebay. This led to spill less than specified in the FOP. Spill at Lower Monumental Dam uses the bulk spill pattern that creates high levels of TDG at low spill volumes. The COE could switch from a bulk spill pattern to a uniform spill pattern and decrease the amount of gas produced. The COE Draft 2013 Annual Report 28 May 2014

44 would not provide uniform spill patterns for the implementation of Court Ordered spill. The COE did agree to include that operation in the spill priority list (as a second priority) developed for the distribution of excess generation spill. In the Regional Implementation Oversight Group discussions in early June, it was decided that spring spill to the gas cap would continue through June 20 th at Lower Monumental Dam. Earlier the COE had expressed a desire to switch to summer spill levels of 17 Kcfs beginning June 4 th, for performance standards testing. However, while still spilling to the gas cap, gas cap spill at Lower Monumental Dam during early June was decreased from 29 Kcfs to 24 Kcfs to address the TDG in the Ice Harbor Dam forebay. While the tailrace TDG had been reduced to 114%, the TDG at the Ice Harbor forebay remained at 118%. This illustrates the difficulty of managing to forebay monitors, which are usually more sensitive to local changes in temperature and primary productivity than to upstream TDG changes. The spill during the summer period generally met the 17 Kcfs during July, except during the hours when spill had to be reduced to accommodate the loading and moving of the fish transportation barges (Figure 3.6). These show up as slight excursions from the 17 Kcfs on the graph. During August the flows were so low that the allowed operation of one turbine unit precluded the ability to provide the full 17 Kcfs spill. Later in August the COE could not maintain RSW spill along with minimum generation flows without causing the project to draft below Minimum Operating Pool. Through the TMT process ( TMT Meeting) the COE coordinated modified spill patterns that do not utilize the RSWs, but instead primarily attempt to focus limited spill to provide attraction for adult fish passage. At Little Goose, Lower Monumental, and Ice Harbor dams spill levels will be the difference between project inflows and the amount of water needed to provide minimum generation through the powerhouses. The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure 3.7. Draft 2013 Annual Report 29 May 2014

45 Figure 3.6. Lower Monumental Dam (LMN) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure 3.7. Historic spill at Lower Monumental Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. Draft 2013 Annual Report 30 May 2014

46 Ice Harbor Dam Spring and summer spill for fish passage occurred according to the Court s Order. The 2013 FOP rolls over the spill operations that have occurred since 2005 and, therefore, the same simulated study test operations that occurred in 2008 was implemented. (The 2013 court ordered operation was a study-like condition). Spill occurred from April 3 rd to April 27 th as 45 Kcfs during the day and spill to the gas cap during nighttime hours. The implementation of study-like conditions at Ice Harbor Dam began on April 28th, and spill alternated between 30% spill for 24 hours and 45 Kcfs daytime spill and gas cap nighttime spill (or that in excess of the operation of one turbine unit), in 2-day blocks until July 13 th. After the completion of the simulated study conditions, spill was provided as 45 Kcfs during daytime hours and spill to the gas cap during nighttime hours, until decreasing flows prevented providing the Court Order within the constraint of operating one turbine unit (powerhouse minimum flow) (Figure 3.8). Figure 3.8. Ice Harbor Dam (IHR) flow and actual spill levels compared to the court ordered spill levels for spring and summer of The implementation of study like conditions in 2013 in a rolled over Fish Operations Plan was again troublesome for fish passage, since spill passage efficiency (SPE) is reduced under part of the study-like conditions. While the implementation of this study-like condition results in less overall spill at this project and is therefore a benefit to power production, the tests conducted in 2006 through 2008 (all with RSW in place) revealed that the reduced spill levels (30% 40% spill) resulted in lower estimates of SPE than the higher spill operations (45 Kcfs/Gas Cap) for both yearling Chinook and steelhead (NOAA, 2008). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure 3.9. Draft 2013 Annual Report 31 May 2014

47 Figure 3.9. Historic spill at Ice Harbor Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. b) Middle Columbia River McNary Dam In 2013 spring spill was initiated on April 10 th and continued to June 20 th. Spring spill was planned as 40% of river flow for 24 hours/day. There were turbine outages throughout the spring and summer, limiting powerhouse capacity. The high river flows that occurred, for flood control operations and the limited hydraulic capacity of the project, resulted in uncontrolled spill in excess of hydraulic capacity in early April. Spill again exceeded the 2013 FOP when flows increased in May, exceeding the hydraulic capacity of the project. The COE initiated the planned summer spill at 50% for 24 hours beginning on June 21 st. Once uncontrolled spill ended when flow decreased, spill continued through August 31 st at the Court Ordered spill levels of 50% of instantaneous flow (Figure 3.10). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Draft 2013 Annual Report 32 May 2014

48 Figure McNary Dam (MCN) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure Historic spill at McNary Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. Draft 2013 Annual Report 33 May 2014

49 John Day Dam Spill was provided from April 10th through August 31 st for spring and summer migrants as specified in the 2013 FOP. Spring spill occurred as 30% of instantaneous flow until the initiation of the spring test, which alternated between 30% spill and 40% spill. The planned test at John Day Dam was designed to start on the evening of April 27 th, at which time spill at John Day Dam would alternate between 30% and 40% of instantaneous flow, roughly every 2 days. Some uncontrolled spill occurred during early May. Summer spill operations resumed the test operations alternating 30% spill and 40% spill as flows receded, and continued through July 20th (Figure 3.12). From July 20 th to August 31 st spill continued as 30% of instantaneous flow. The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Figure John Day Dam (JDA) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Draft 2013 Annual Report 34 May 2014

50 Figure Historic spill at John Day Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. The Dalles Dam Spring spill began on April 10th and summer spill continued through August 31, 2013 (Figure 3.14). Spring and summer spill were provided as 40% of instantaneous flow, except when spill percentages were adjusted downward based on TDG measurements in the Bonneville Dam forebay that occurred at times during early May. The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Draft 2013 Annual Report 35 May 2014

51 Figure The Dalles Dam (TDA) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Figure Historic spill at The Dalles Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. Draft 2013 Annual Report 36 May 2014

52 Bonneville Dam Spill was planned from April 10th through June 15 th at 100 Kcfs for 24 hours a day. Due to high flows, spill at Bonneville Dam exceeded the planned spill levels during early May. Spill was also less that the planned 100 Kcfs during some periods in the spring due to managing TDG levels at the Camas/Washougal TDG gage. On June 16 th the summer spill program was initiated at Bonneville Dam, 15 days earlier than normal, for research purposes. Spill was managed to the study objectives of 95 Kcfs for 24 hours versus 85 Kcfs during daytime hours and 121 Kcfs during nighttime hours. Beginning July 21st, the project reverted to the 2013 FOP level of 75 Kcfs during daytime hours and gas cap spill at night (Fig. 3.16). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Figure Bonneville Dam (BON) flow and actual spill levels compared to the court ordered spill levels for spring and summer of Draft 2013 Annual Report 37 May 2014

53 Figure Historic spill at Bonneville Dam as a proportion of total flow for the years 1981 to 2013 for both the spring and summer period. c) Upper Columbia River Fish passage operations through the upper Columbia River are managed under the terms of different agreements separate from the FCRPS Biological Opinion. The fish passage operations for Wells Dam are operated under the auspices of the Douglas County Public Utility District Habitat Conservation Plan (PUD No. 1 of Douglas County, 2013); fish passage operations for Rocky Reach and Rock Island dams are operated under the auspices of the Chelan County Public Utility District Habitat Conservation Plan (PUD No. 1 of Chelan County et al., 2013); the fish passage operations at Priest Rapids and Wanapum dams are operated under the auspices of a separate settlement agreement. All of these projects operate under the terms of Federal Energy Regulatory Commission licenses. Draft 2013 Annual Report 38 May 2014

54 Grand Coulee and Chief Joseph High runoff periods resulted in some spill from the Grand Coulee Dam. Chief Joseph Dam is used to manage flow from Grand Coulee Dam in such a way as to minimize spill at Grand Coulee. The water that should have been spilled at Grand Coulee is transferred to Chief Joseph Dam, which is equipped with flow deflectors that minimize the amount of total dissolved gas that is produced and discharged into the Upper Columbia River. Some spill occurred at times from April through June at this project. Figure Grand Coulee Dam daily average flow and actual spill levels for spring and summer of Figure Chief Joseph Dam daily average flow and actual spill levels for spring and summer of Wells Dam The operation of the Wells Dam bypass system provides juvenile fish passage at this project. The bypass was operated from April 9 th to August 19 th for juvenile fish passage. At times flow through the bypass exceeded the 10 Kcfs, as river flow exceeded hydraulic or Draft 2013 Annual Report 39 May 2014

55 generation capacity (Figure 3.20). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Figure Wells Dam daily average flow and actual spill levels for spring and summer of Figure Historic spill at Wells Dam as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period. Draft 2013 Annual Report 40 May 2014

56 Rocky Reach Dam In the spring of 2013, Rocky Reach Dam was operated with the juvenile fish bypass, and some spill, due to high river flows. The spill was due to excess hydraulic capacity and excess generation. Planned summer spill at Rocky Reach was for 9% of daily average flow from June 5 th to August 21 st. However, at times spill was in excess of the 9% due to excess hydraulic capacity or excess generation spill (Figure 3.22). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Figure Rocky Reach Dam daily average flow and actual spill levels for spring and summer of Draft 2013 Annual Report 41 May 2014

57 Figure Historic spill at Rocky Reach Dam as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period. Rock Island Dam Spring spill at Rock Island Dam began on April 17 th and continued until June 4 th as 10% of daily average flow. Rock Island fish spill increased to the mandated 20% for the summer outmigration of subyearling Chinook on June 5 th and continued through August 18 th (Figure 3.24). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Draft 2013 Annual Report 42 May 2014

58 Figure Rock Island Dam daily average flow and actual spill levels for spring and summer of Figure Historic spill at Rock Island Dam as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period. Draft 2013 Annual Report 43 May 2014

59 Wanapum Dam The Wanapum Future Unit Fish Bypass was operated for fish passage during the spring and summer fish passage period (April 17 to August 22). At a tailwater elevation of feet or higher, the Wanapum Future Unit Fish Bypass is operated to pass 20 Kcfs of water. However, due to high flows, spill occurred in excess of hydraulic capacity, or in excess of generation needs (Figure 3.26). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Figure Wanapum Dam daily average flow and actual spill levels for spring and summer of Draft 2013 Annual Report 44 May 2014

60 Figure Historic spill as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period. Priest Rapids Dam During the 2013 smolt out-migration season, the Priest Rapids Top-Spill Operations Configuration spill program used in both 2010 and 2011 was followed with the only exception that spill operations were moved to spill gates 4 7 to accommodate the construction of the Priest Rapids Fish Bypass. This spill operation consisted of 6.8 kcfs surface spill through the top spill bulkhead at spill bays 5 and 6, and 5 kcfs bottom spill through tainter gates 4 and 7 each. With this configuration, the total fish spill amount was approximately 24 kcfs. Involuntary spill was passed through the remaining spillway gates at Priest Rapids. Fish spill began on April 18 and ended on August 23, 2013 (Figure 3.28). The 2013 and historic spring and summer spill as a proportion of total flow is shown in Figure Draft 2013 Annual Report 45 May 2014

61 Figure Priest Rapids Dam flow and actual spill levels for spring and summer of Figure Historic spill as a proportion of total flow for the years 1997 to 2013 for both the spring and summer period. Draft 2013 Annual Report 46 May 2014

62 4. Summary and Conclusions Spill in 2013 in the FCRPS was provided according to the Fisheries Operations Plan for The Fish Operation Plan modified the 2013 spill implementation roll over of 2012 operations to accommodate new structures and research. This operational plan was made into a Court Order on March 28, 2013, for both the spring and summer operations. Flows in 2013 were much closer to average than in 2011 and Consequently, only small amounts of uncontrolled spill occurred during high runoff periods. Spill at Lower Monumental Dam was consistently constrained by the COE due to TDG, rather than changing spill patterns as recommended by the fishery agencies and tribes. Planned summer spill levels were implemented early at a number of the federal hydroelectric projects in order to conduct summer spill research when greater numbers of fish were present. Spill plans at the Upper Columbia projects varied from no spill to fixed volumes or percentages during spring and summer. Given the importance of spill in the survival of fish to adulthood, spill continues to be an important mitigation tool. B. Gas Bubble Trauma (GBT) Monitoring and Data Reporting for Overview The goal of the juvenile salmonid GBT monitoring program is to determine the relative extent that migrating juvenile salmonids have been exposed to harmful levels of total dissolved gas. The determination is based upon the prevalence and severity of GBT-induced bubbles on the fish. The data are reported to the fisheries management entities, the water quality agencies of Washington and Oregon, and are available to other interested parties through Fish Passage Center weekly reports and daily postings to the FPC web site during the season ( The monitoring of juvenile salmonids in 2013 for GBT was conducted at Upper Columbia, Middle Columbia, and Snake River sites. Fish were collected and examined for signs of GBT at Bonneville Dam and McNary Dam on the Middle Columbia River, and at Rock Island Dam on the Upper Columbia River. The Snake River monitoring sites were Lower Granite, Little Goose and Lower Monumental dams. Sampling occurred two days per week at the Columbia River sites and one day a week at each of the Snake River sites throughout the spring and summer spill programs. Draft 2013 Annual Report 47 May 2014

63 The goal of the sampling program was to sample 100 salmonids of the most prevalent species (limited to chinook and steelhead) during each day of sampling at each site, with the proportion of each species sampled dependent upon their prevalence at the time of sampling. Yearling Chinook and steelhead were sampled through the spring at all the sampling sites. Once subyearling Chinook predominated in the smolt collections, the program shifted from sampling yearling Chinook and steelhead to sampling subyearling Chinook, which continued through the end of August unless an adequate sample could not be collected. In this case, sampling for GBT may have ended prior to the end of August. Examinations of fish were done using variable magnification (6x to 40x) dissecting scopes. The eyes and unpaired fins were examined for the presence of bubbles. The bubbles present were quantified using a ranking system based on the percent area of the fins or eyes covered with bubbles (Table 3.2). Table 3.2. Ranking criteria used in monitoring for signs of gas bubble trauma. Rank Sign 0 no bubbles present 1 up to 5% of a fin area or eye covered with bubbles 2 6% to 25% of a fin area or eye covered with bubbles 3 26% to 50% of a fin area or eye covered with bubbles 4 > than 50% of a fin area or eye covered with bubbles Additional information was recorded for each fish, including species, age, fork length, fin clips, and tags. The examination procedures were similar to those used in past years of the program (see the GBT Monitoring Protocol ftp://ftp.fpc.org/gbt/ for details of exam procedures). All sampling sites were at dams where fish could be collected from the juvenile fish bypass system. Fish to be examined for GBT were collected at the separator at juvenile salmonid transportation collection sites, and by the standard collection methods at Rock Island and Bonneville dams. The January July runoff volume for the 2013 water year was near average in the Lower Columbia River but below average in the Lower Snake River. Runoff (January July) was 96% of average ( ) at the Dalles Dam and 69% of average at Lower Granite Dam. In the Snake River, this resulted in mostly lower than average flows throughout the spring and summer seasons, with peak flows in May (Figure 3.30). In the Lower Columbia, the 2013 runoff resulted in near average flows in both the spring and summer periods (Figure 3.31). The peak flow conditions in the Snake River and Lower Columbia rivers in mid-may resulted in uncontrolled spill for a few days at the Snake and Columbia River sites. At times TDG levels were slightly above the TDG waiver levels during this time period. Draft 2013 Annual Report 48 May 2014

64 Figure Average daily flows at Lower Granite Dam 2013, 2012, and the 10-year average. Figure Average daily flows at McNary Dam 2013, 2012, and the 10-year average. Draft 2013 Annual Report 49 May 2014

65 2. Results In all, 13,558 juvenile salmonids were examined for GBT between April and August of 2013 (Table 3.3). The fish were collected as part of the Smolt Monitoring Program. Table 3.3. Number of juvenile salmonids examined for signs of GBT at dams on the Lower Snake River and on the Columbia River from April to August 2013 as part of the GBT Monitoring Program. Species BON MCN LMN LGS LGR RIS Total Chinook Subyearlings 1,575 2, ,023 6,112 Chinook Yearlings 1,036 1, ,913 Steelhead ,533 Total 2,868 3,814 1,843 1, ,412 13,558 Fin signs were found in 42 or 0.31% of the total fish sampled at all sites (Table 3.4). The fish examined and determined to have signs of GBT exhibited the fin signs that were most often rank 1, where less than 5% of a fin area was covered with bubbles. No signs of rank 2 or 3 were seen in 2013, but one fish with rank 4 was encountered at Rock Island Dam in early July. A more detailed breakdown of GBT exams and signs for 2013 can be found in Tables at the end of the chapter. Table 3.4. Number of juvenile salmonids found with fin GBT at dams on the Lower Snake River and on the Columbia River from April to August 2013 as part of the GBT Monitoring Program. Sum of Fin GBT Site Grand Species BON MCN LMN LGS LGR RIS Total CH CH ST Grand Total The action criteria for GBT is established as 15% of fish showing any signs of fin GBT, or 5% of the fish sampled showing signs of fin GBT greater than or equal to rank 3. Neither of these two action criteria was met in Lower Granite Dam (LGR) GBT sampling at LGR occurred from April 9 th to May 28 th. LGR does not sample for GBT when subyearling Chinook predominate the sample. Total dissolved gas (TDG) in the Dworshak Dam tailrace never exceeded 120% in 2013 and TDG in the LGR forebay never exceeded 115%. No signs of GBT were observed at LGR in 2013 (Figure 3.32). Draft 2013 Annual Report 50 May 2014

66 Figure Percent GBT observed in the sample at Lower Granite Dam Little Goose Dam (LGS) GBT sampling at LGS occurred from April 7 th to August 5 th. Sampling was terminated after August 5th at LGS because of the inability to collect the sample necessary to conduct GBT exams. Both the prevalence and severity of GBT signs at LGS were low in Signs of GBT were detected only on four occasions in 2013, with a maximum GBT rate of 1% on each of these four occasions. All incidences of GBT at LGS in 2013 were at the rank 1 level. TDG levels in the LGR tailrace exceeded the 120% criteria for a short period in mid-july and mid-august. In addition, TDG in the LGS forebay exceeded the 115% criteria for brief periods in early May, early July, and mid-august (Figure 3.33). Draft 2013 Annual Report 51 May 2014

67 Figure Percent GBT observed in the sample at Little Goose Dam. Lower Monumental Dam (LMN) GBT sampling at LMN occurred from April 4 th to July 31 st. Sampling was terminated after July 31 st because of the inability to collect the sample necessary to conduct GBT exams. There were no signs of GBT at Lower Monumental Dam in TDG in the LGS tailrace never exceeded 120% in TDG at the Lower Monumental forebay exceeded 115% for a period in early to mid-may (Figure 3.34). Draft 2013 Annual Report 52 May 2014

68 Figure Percent GBT observed in the sample at Lower Monumental Dam. McNary Dam (MCN) GBT sampling at MCN occurred from April 8 th to August 30 th. The TDG levels in the tailraces at Priest Rapids (PRD) and Ice Harbor (IHR) dams exceeded 120% for a very short period in At the IHR tailrace, TDG exceeded 120% for 4 days in mid-may while at the PRD tailrace, TDG exceeded 120% for 2 days in late June/early July (Figure 3.35). TDG at the MCN forebay exceeded 115% for short periods in mid-may and early July. The number of incidences of GBT at McNary Dam in 2013 was higher than what was observed in the Snake River at Little Goose and Lower Monumental dams. In all, there were 16 days where signs of GBT were observed at MCN in Of these, the maximum rate of GBT was 3.0%, which occurred on July 23rd. All of the fish that showed signs of GBT at MCN in 2013 had rank 1 signs. Draft 2013 Annual Report 53 May 2014

69 Figure Percent GBT observed in the sample at McNary Dam. Bonneville Dam (BON) GBT sampling at BON occurred from April 20 th to August 24 th. At Bonneville Dam, there were 5 days in 2013 when signs of GBT in fish were recorded (Figure 3.36). Of these five days, the maximum GBT rate was 2.0%, which occurred on July 30th. All of the fish that exhibited signs of GBT at BON in 2013 had signs that were rank 1. TDG in the tailrace at The Dalles Dam never exceeded 120% in However, TDG in the BON forebay exceeded 115% for brief periods throughout the spill season. The longest continuous period where the BON forebay exceeded 115% was 7 days at the end of May. Draft 2013 Annual Report 54 May 2014

70 Figure Percent GBT observed in the sample at Bonneville Dam. Rock Island Dam (RIS) GBT sampling at RIS occurred from April 15 th to August 18 th. Sampling was terminated after August 18th at RIS because of the inability to collect the sample necessary to conduct GBT exams. There were 8 total days where signs of GBT were detected at RIS in 2013 (Figure3.37). The maximum GBT rate at RIS in 2013 was 3.0%, which occurred on June 5th. Overall, TDG in the Upper Columbia was relatively low in TDG levels in the tailraces of Grand Coulee, Chief Joseph, and Wells dams never exceeded 120% in However, TDG in the tailrace at Rocky Reach Dam (RRH) exceeded 120% for short periods throughout the spill season. The longest continuous period where the TDG in the RRH tailrace exceeded 120% was 8 days, from June 28 th to July 5 th. Among the various forebay monitors above RIS, only those in the RRH forebay and RIS forebay had TDG levels that exceeded 115%. Of the 11 fish that showed signs of GBT at RIS in 2013, all but one was rank 1. (A single fish was recorded with rank 4 signs in its anal fin, however, based on past experience we would not have expected to observe these signs at the prevailing TDG levels. It is possible that this was an incorrect data entry, but it could not be verified that this was the case. Consequently, the observation was retained in the database.) Draft 2013 Annual Report 55 May 2014

71 Figure Percent GBT observed in the sample at Rock Island Dam. Table 3.5 compares the 2013 estimates of the overall percentage of fish with signs of GBT to past years estimates. This is not meant as a measurement of overall GBT, but is used to easily display the annual relative magnitude of GBT in 2013 compared to past years. As can be seen in the table the overall annual incidence of GBT in 2013 was in the lower-range among the past 17 years. Draft 2013 Annual Report 56 May 2014

72 Table 3.5. Percent of sampled fish with signs of fin GBT estimated for the total fish observed in each year 1996 to Year Total % Signs % Signs excluding RIS Discussion The Biological Opinion Spill Program is managed, whenever possible, using the data collected for TDG levels. The GBT biological monitoring is meant to complement the physical monitoring program. GBT sampling was successfully accomplished for the 2013 migration season. The GBT monitoring program has consistently shown over the years of implementation that signs of GBT are minimal when TDG is managed to the criteria levels of 115/120% TDG. Historically signs of GBT do not approach the action criteria until TDG levels are near 130% supersaturation levels in the tailraces or forebays of dams. The 2013 TDG was managed close to the 115/120% criteria, and the low incidence of signs of GBT observed this year reflects that management. Draft 2013 Annual Report 57 May 2014

73 References Haeseker, S.L., J.M. McCann, J.E. Tuomikoski, and B. Chockley Assessing freshwater and marine environmental influences on life-stage-specific survival rates of Snake River spring/summer Chinook salmon and steelhead. Transactions of the American Fisheries Society, 141:1, NOAA Fisheries, Northwest Fisheries Science Center, Passage Behavior and Survival for radio-tagged subyearling Chinook salmon at Lower Monumental and Ice Harbor dams, Preliminary Results. Petrosky, C. and H. Schaller Influence of river conditions during seaward migration and ocean conditions on survival rates of Snake River Chinook salmon and steelhead. Ecology of Freshwater Fish 19: Public Utility District No. 1 of Chelan County Wenatchee, Washington, Public Utility District No. 2 of Grant County, Washington. Summary of 2013 annual fish spill season and total dissolved gas monitoring. GCPUD%20FINAL_TDG- SpillSeason_Report_2013_10_31%20(4).pdf Public Utility District No. 1 of Douglas County Wells Hydroelectric Project Total Dissolved Gas Abatement Plan 2013 Annual Report. %20Final%20TDG%20Annual%20Report%202013%20season%20(GAP%20report).pdf Schaller, H. and S. Haeseker. Environmental and management influenced variables affect survival rates. Comparative Survival Study Annual Review. April 2, Schaller, H.A., C.E. Petrosky, and E.S. Tinus Evaluating river management during seaward migration to recover Columbia River stream-type Chinook salmon considering the variation in marine conditions. Can. J. Fish. Aquat. Sci. 71(2) Scheurell, M. and R. Zabel Seasonal differences in migration timing lead to changes in the smolt-to-adult survival of two anadromous salmonids. Northwest Fisheries Science Center. Tuomikoski, J., J. McCann, T. Berggren, H. Schaller, P. Wilson, S. Haeseker, C. Petrosky, E. Tinus, T. Dalton, and R. Elke Comparative Survival Study (CSS) of PIT tagged Spring/Summer Chinook and Summer Steelhead, 2009 Annual Report. Project No Final.pdf Tuomikoski, J., J. McCann, T. Berggren, H. Schaller, P. Wilson, S. Haeseker, J. Fryer, C. Petrosky, E. Tinus, T. Dalton, and R. Ehlke Comparative Survival Study (CSS) of PIT-tagged Spring/Summer Chinook and Summer Steelhead, 2010 Annual Report, Project No Draft 2013 Annual Report 58 May 2014

74 Tuomikoski, J., J. McCann, T. Berggren, H. Schaller, P. Wilson, S. Haeseker, J. Fryer, C. Petrosky, E. Tinus, T. Dalton, and R. Ehlke Comparative Survival Study (CSS) of PIT-tagged Spring/Summer Chinook and Summer Steelhead, 2011 Annual Report, Project No Tuomikoski, J., J. McCann, B. Chockley, H. Schaller, P. Wilson, S. Haeseker, J. Fryer, C. Petrosky, E. Tinus, T. Dalton, and R. Ehlke Comparative Survival Study (CSS) of PIT-tagged Spring/Summer Chinook and Summer Steelhead, 2012 Annual Report, Project No Tuomikoski, J., J. McCann, B. Chockley, H. Schaller, S. Haeseker, J. Fryer, R. Lessard, C. Petrosky, E. Tinus, T. Dalton, and R. Ehlke Comparative Survival Study (CSS) of PIT-tagged Spring/Summer Chinook and Summer Steelhead, 2012 Annual Report, Project No USACE Fish Operations Plan, U.S. Army Corps of Engineers, March 9, USACE. Flow, Spill and TDG data. U.S. Army Corps of Engineers Water Control Data. Washington State Department of Ecology and State of Oregon Department of Environmental Quality Adaptive Management Team Total Dissolved Gas in the Columbia and Snake Rivers, Evaluation of the 115 Percent Total Dissolved Gas Forebay Requirement. January 2009 Publication no Draft 2013 Annual Report 59 May 2014

75 IV Smolt Monitoring A. Summary Flows were relatively low in the Snake River in 2013, and near average to above average in the Columbia River, which led to better than average migration conditions for migrant juvenile salmonids in the Rock Island to McNary Dam reach, but below average flow conditions in the Snake River. Tuomikoski et al. (2012) concluded in their analysis of reach survival that their analyses indicated The instantaneous mortality rates tend to be lowest under conditions of fast water transit time (WTT) and high spill levels. In addition, mortality rates tend to increase over the migration season. We found some evidence that the increased number of dams with surface passage structures in the spillways may be reducing mortality rates. The combination of factors that influence fish travel time and instantaneous mortality are the factors that influence survival. The reach survivals in 2013 generally reflected the conditions seen during outmigration. In general lower flows in the Snake River were compensated by higher spill proportions in the reach, leading to near average survivals for most groups. In the Rock Island Dam to McNary Dam reach, where flows were near or slightly above average, nearly all survivals, for all species, were at or above the long-term averages. For many cohorts of Snake River yearling Chinook, subyearling Chinook, sockeye and steelhead, survivals in 2013 were generally near average for the time series 1998 to 2012, with some cohorts above the long-term average and others below. Fish travel times for the Snake River cohorts also were near average with some longer and some more rapid than the long-term average. The presence of surface spill structures at all dams in the reach likely contributed to the observed survivals, particularly for steelhead and subyearling Chinook, especially considering the average to lower than average flows most groups experienced. Similar to 2012, sockeye and subyearling Chinook survivals in the Rock Island Dam to McNary Dam reach were above the long-term average. Water transit times were more rapid than average for the sockeye and subyearling cohorts and spill percentages were at or above average resulting in better than average migrating conditions. For yearling Chinook and steelhead in the reach, survivals were near average. Draft 2013 Annual Report 60 May 2014

76 B. Special Operations at Sites in the Lower Snake and Lower Columbia in 2013 The start date of spring transportation was earlier in 2013 than in previous years. Transportation began on April 28 th at Lower Granite Dam, with collected fish bypassed back to the river prior to the initiation of transportation. This resulted in a higher portion of fish in transport barges when compared to when transportation was delayed to allow a proportion of spring migrants to migrate in-river. The start of transportation was staggered at the collection sites in the Snake River, with Lower Granite Dam beginning collection for transport on April 27 th, May 2 nd at Little Goose Dam, and May 7 th at Lower Monumental Dam. For the ninth year, court ordered summer spill occurred at all Snake River dams as well as McNary. Overall the probability of transport during the migration season ranged from 30% for hatchery subyearling Chinook to 61% for wild subyearling Chinook (Table G.9). Details of the number and proportion of fish transported can be found in Appendix G. Juvenile fish compliance monitoring for subyearling Chinook occurred at Little Goose and Lower Monumental dams in 2013 and those activities are summarized below. The objectives of these studies were to measure the survival of acoustically tagged fish at the dams to determine if the Biological Opinion (BiOp) compliance criteria for fish survival had been met, as well as to measure Fish Accord criteria. All subyearling Chinook used in 2013 performance testing was collected at Lower Monumental Dam and tagged with acoustic tags. The metrics evaluated in these studies were limited to survival at the project as well as passage efficiency by route. The methodology for these studies can be found in Skalski (2009). Concerns were raised in 2013 about artificial inflation of survival estimates due to the use of multiple control groups, high rejection rates of tagged fish, and differences in survival under spring and summer operations. These studies do not assess the impact of various passage structures and passage operations on the other life-cycle stages such as smolt-to-adult returns (SARs). Results of route of passage acoustic survival studies and route of passage SAR data at McNary Dam, conducted in the same juvenile out-migration years, indicated that acoustic tag results at the project did not reflect the smolt-to-adult return rate by route of passage (Ferguson 2006). The acoustic tag survival estimates showed lesser impacts of bypass passage in relation to spillway passage when measuring short reach survival estimates than those from SAR data comparisons. The acoustic-tag data discussed below are only one component of the decision framework involved in understanding the impacts of dam operations on overall smolt-to-adult returns. Draft 2013 Annual Report 61 May 2014

77 1. Lower Granite Dam (LGR) Fish were collected and transported on April 26 th for research purposes, and regular collection for transport at this site began on April 27 th. Transportation began on April 28 th and was every other day until May 2 nd, when daily barging began. Every other day transport resumed on June 4 th, so on alternate days fish were held an extra day prior to transport. Summer spill occurred for the eighth consecutive year based on the Court order. Spill started on April 3 rd as planned. Spill continued until August 31 st at the project, also as planned. A study in 2013 was conducted to evaluate the prototype juvenile fish collection channel overflow weir and enlarged orifice. This study used PIT-tagged clipped yearling Chinook, steelhead, and subyearling Chinook that were collected as part of the Smolt Monitoring Program and re-released above the juvenile bypass intake. Some of these test fish returned to the SMP facility, where their inclusion in counts marginally inflated estimates of passage and population indices. 2. Little Goose Dam (LGS) Collection and transport began on May 3 rd at Little Goose Dam. Prior to that date, sampling was performed in support of condition sampling and GBT sampling was conducted once every 5 days. Collection for every other day transport began on June 4 th as fish numbers declined. Spring spill had a planned and actual start date of April 3 rd, and ended on August 31 st. In 2013 a study was planned to use acoustic tags to measure subyearling Chinook survival at the dam, as well as other passage metrics such as spill passage efficiency. The study was conducted from June 4 th to July 6 th. Normal operations of 30% were used throughout the test. The concrete survival estimates was 90.76%, which does not meet the performance standard requirement of 93%. A new top spillway weir (TSW) was installed at this project in 2009 and used through The weir design allowed it to be operated at two elevations: 15 feet or 11 feet at minimum operating pool elevation (633 feet). The TSW was changed from high to low crest on May 9 th, earlier than in previous years due to an inability to change TSW operations during juvenile performance testing. 3. Lower Monumental Dam (LMN) Collection for transport began on May 7 th and the first barge was loaded on May 8 th. Prior to the start of transportation, sampling was performed in support of condition sampling every 3 days. Collection for every other day transport began on June 4 th as fish numbers declined. Draft 2013 Annual Report 62 May 2014

78 Spring spill had a planned start date of April 3 rd, and started as planned. Spill ended on August 31 st. In 2013 a study was planned to use acoustic tags to measure subyearling Chinook survival at the dam, as well as other passage metrics such as spill passage efficiency. The study was conducted under spring spill operations of spill to the gas cap from June 4 th to June 21 st, and summer spill operations of 17 Kcfs from June 21 st to July 6 th. The season-wide survival estimate was 92.97%, which does not meet the performance standard requirement of 93%. The Removable Spillway Weir (RSW) was installed in 2008 and operated again in Although requests were made to spill in the uniform pattern to maintain court-ordered spill levels and avoid violation of total dissolved gas requirements, spill remained in the bulk pattern and was reduced to maintain total dissolved gas levels. 4. Ice Harbor Dam (IHR) Study operations were again implemented in 2013 as a rollover operation, as in , but no research occurred. Spring spill started on April 3 rd, as planned. Summer spill ended on August 31 st. Alternating operations began on April 29 th and continued through July 13 th. These alternating operations were a reduced spill (30% of total discharge) versus BiOp spill levels (which were 45 Kcfs day/gas cap night) or 64% spill operation. 5. McNary Dam (MCN) The barging program for subyearling Chinook at McNary dam was discontinued, starting in Spring spill had a planned start date of April 10 th but actually started on April 1 st due to flows in excess of hydraulic capacity. Both TSW units in spillbays 19 and 20 were used during the spring fish passage season for the sixth year. They were removed before the start of the summer season. 6. John Day Dam (JDA) In 2013 there were no studies to evaluate 30% and 40% spill operations, but alternating operations were carried out anyway. Spring spill had a planned start date of April 10 th but actually started on April 8 th due to high flows. 7. The Dalles Dam (TDA) Spring spill had a planned start date of April 10 th, but actually started on April 8 th due to high flows. Draft 2013 Annual Report 63 May 2014

79 8. Bonneville Dam (BON) Spring spill had a planned start date of April 10 th but actually started on April 7 th due to high flows. Condition monitoring at Bonneville Dam indicated that higher descaling and mortality arose when turbines in Powerhouse 2 were operated at the higher end of the 1% range. To reduce these effects, Powerhouse 2 was limited to the lower range of the 1% until maximum capacity at Powerhouse 1 was reached. When best geometry was reached at Powerhouse 1, flows through Powerhouse 2 were then increased. C. Overview of Travel Time and Survival Under 2013 Conditions 1. Snake River In general lower flows in the Snake River were compensated by higher spill proportions in the reach, leading to near average survivals for most groups. For many PIT-tag cohorts of Snake River yearling Chinook, subyearling Chinook, sockeye and steelhead, survivals in 2013 were generally near average for the time series 1998 to 2012, with some cohorts above the long-term average and others below. Fish travel times for the Snake River cohorts also were near average with some longer and some more rapid than the long-term average. The presence of surface spill structures at all dams as well as higher than average spill operations at the dams in the reach likely contributed to the observed survivals, particularly for steelhead and subyearling Chinook, especially considering the average to lower than average flows most groups experienced. 2. Mid Columbia River Similar to 2012, sockeye and subyearling Chinook survivals in the Rock Island Dam to McNary Dam reach were above the long-term average. Water transit times were more rapid than average for the sockeye and subyearling cohorts and spill percentages were at or above average resulting in better than average migrating conditions. For yearling Chinook and steelhead in the reach, survivals were near average. 3. Lower Columbia River In the McNary to Bonneville Dam reach flows were slightly above average for the PIT-tag cohorts as were the spill proportions these groups encountered. The estimated survivals for hatchery and wild yearling Chinook and hatchery and wild steelhead PIT-tag cohorts in the reach were mostly above the long-term average for the years 1999 to Fish travel times for all cohorts were more rapid than the long-term average as well reflecting the relatively good in-river conditions. Draft 2013 Annual Report 64 May 2014

80 D. Smolt Monitoring Sites and Schedules for 2013 and Methods for Analyses 1. Smolt Monitoring Sites and Schedules for 2013 Information on the juvenile salmon out-migration is collected each year to aid the Fisheries Agencies and Tribes in making management decisions beneficial to smolt survival as they move downriver from natal streams, through the hydrosystem and on toward the ocean. The Smolt Monitoring Program (SMP) provides data on the initiation of the juvenile out-migration, estimates of relative fish abundance at the dams, migration timing at traps and dams, fish travel time through key river reaches both prior to and within the hydrosystem, and estimates of survival for key groups of fish through index reaches. Portions of the data are gathered on the run-at-large migrating population, such as the passage indices, while other data such as travel time and survival estimates target specific mark-groups of fish. All of the data are collected for the purpose of providing information for management of flows and spill, and post-season evaluation of the effects of the year s management actions on migrating juvenile salmonids. Because the SMP has been carried out over the course of 20 years or more at some locations, the program also provides historic perspective for comparison of both in-season data with past years and for combining recent data with historic data for retrospective analyses. Data were gathered at eleven monitoring sites in the Columbia River Basin (See Table 4.1 for sites and dates of operation for 2013). Monitoring was conducted at four traps in the Snake River Basin above Lower Granite Dam, three dams in the Lower Snake River, Rock Island Dam in the mid-columbia River, and three dams in the Lower Columbia River. Data from all sites were transmitted to FPC daily during the sampling season, where they were archived as well as compiled for reporting. In addition to collection monitoring information, fish are PIT-tagged at all four SMP traps, Rock Island Dam, and at selected hatcheries for more specific evaluations. The monitoring information was made available to all interested parties via the FPC web page at Data were also available through the FPC s weekly reports or by data requests made to FPC staff. Draft 2013 Annual Report 65 May 2014

81 Table 4.1. Smolt monitoring sites and schedules for Site Sampling Method Dates of Operation Primary Fish Data Bonneville Dam (BON) PH2: Timed sub-sample from bypass Mar. 13 to Oct. 12 C, FQ, GBT(2) John Day Dam (JDA) Timed sub-sample from bypass Apr. 1 to Sept. 15 C, FQ McNary Dam (MCN) Timed sub-sample from bypass Apr. 7 to Sept. 30 C, FQ, GBT(2) Lower Monumental Dam (LMN) Timed sub-sample from bypass Apr. 1 to Oct. 1 C, FQ, GBT(1) Little Goose Dam (LGS) Timed sub-sample from bypass Apr. 3 to Oct. 31 C, FQ, GBT(1) Lower Granite Dam (LGR) Rock Island Dam (RIS) Snake River Trap (LEW) (rkm 225) Salmon River Trap (WTB) (rkm 123) Grande Ronde Trap (GRN) Timed sub-sample from bypass Mar. 26 to Oct. 31 C, FQ, GBT(1) PH2: Census of fish captured in volitional bypass Apr. 1 to Aug. 31 C, FQ, GBT(2), PIT Rotating Drum Dipper Trap Mar. 4 to May 15 C, FQ, PIT Inclined Plane Trap Mar. 4 to May 8 C, FQ, PIT Inclined Plane Trap Mar. 6 to May 22 C, FQ, PIT Imnaha Trap (IMN) 1 2 Screw Traps Mar. 11 to Jul. 18 C, FQ, PIT C = fish counts recorded. FQ = fish quality including descaling and/or injury data obtained. GBT(k) = gas bubble trauma measurements taken k days per week. PIT = PIT-tagging and release from site. Upon the request of the ISAB and the Lamprey Technical Workgroup, larval and juvenile lamprey have been included as target species in the Smolt Monitoring Program. The Imnaha trap began including larval and juvenile lamprey as target species in As target species, larval and juvenile lamprey are identified to one of five categories: (1) Pacific ammocoete, (2) western brook ammocoete, (3) unknown ammocoete, (4) Pacific macropthalmia, and (5) unidentified lamprey. Treating larval and juvenile lamprey as target species of the SMP allowed for the expansion of lamprey samples to an estimated collection. However, unlike salmonids, a passage index was not estimated for juvenile and larval lamprey. 2. Methods: Collection Estimates and Passage Index Collection estimates are the total number of juvenile salmonids calculated to have entered the bypass at a particular dam. The collection estimate is derived from timed sub-samples taken at intervals throughout a daily 24- hour period. The timed sub-sample is determined by the sample rate(s) that are used at each site, on a daily basis. Therefore, the collection estimate is calculated by dividing the daily catch by the sample rate that was used that day (Table 4.2). Draft 2013 Annual Report 66 May 2014

82 The daily passage index is computed by dividing the daily collection by the proportion of water passing through the powerhouse where the sampling takes place (Table 4.2). The daily passage indices adjust for daily changes in spill proportion under the conservative assumption that the proportion of fish passing through spill will be close to the proportion of water being spilled. Estimates of fish guidance efficiency of the screens or of spill efficiency (proportion of fish passing through spill) are not necessary using this method. As long as the daily passage index remains highly correlated to daily population abundance at each site, the passage index remains useful for gauging passage timing and magnitude of passage. The passage index is not applicable to trap sites because collection efficiencies of the traps are not calculated; therefore only collection counts are reported for the four SMP traps. Table 4.2. Formulas to compute passage indices (collection estimate/flow expansion factor) at dams. Sampling Site Years Collection Estimate Passage Index Rock Island Dam (PH 2) Catch/1 Coll*((PH1+PH2+SP)/(PH2)) Lower Granite Dam Little Goose Dam Lower Monumental Dam McNary Dam John Day Dam (bypass) John Day Dam Unit Catch/sample rate Coll*((PH+SP)/(PH)) Catch/sample rate Catch/1 Coll*((PH+SP)/(PH)) Coll*((PH+SP)/(PH)) Bonneville Dam (PH 1) hr catch/sample rate 24-hr catch/sample rate Coll*((PH1+PH2+SP)/(PH1)) hr catch/sample rate Bonneville Dam (PH 2) hr catch/sample rate Coll*((PH1+PH2+SP)/(PH2)) Legend: Coll=Collection Estimate; PH=powerhouse flow; PH1=first powerhouse flow; PH2=second powerhouse flow; SP=spill flow; and Unit3=turbine unit 3 flow (note: all flows are 24-hour averages over the sample interval). 3. Methods: Population Index The population index is an in-season tool that uses predictions of daily PIT-tag detection probability (i.e., probability of entering the collection or bypass facility) based on daily flow and spill percentage data. Here, detection probability, or the probability of PIT-tagged fish being detected at the dam, is believed to be equal to the probability of untagged fish entering the fish collection (or bypass) system. This is because the PIT-tag detection system is located in the bypass where detection probability is virtually 100%. Population indices have been generated for Lower Granite Dam for this report although indices are also available for Little Goose Dam via the FPC web page. Specifically, daily collection estimates generated by the SMP at Lower Granite Dam were divided by predicted daily detection probability (analogous to collection probability) to generate daily population estimates. The methodology used to predict daily PIT- Draft 2013 Annual Report 67 May 2014

83 tag detection probability is beyond the scope of this annual report. However, these methods are described in detail in a technical memorandum available on the FPC web page ( The population index is believed to be more accurate than the passage index for estimating the magnitude of the population because it does not assume 1:1 fish to water ratio that is inherent in the passage index expansion. However, comparisons to population estimates (see below for these methods) typically show the cumulative population index results in a higher total. 4. Methods: Population Estimate Annual population estimates were generated for yearling Chinook and steelhead at Lower Granite Dam in this report (Tables 4.5 through 4.8). These population estimates were generated by taking the annual estimate of smolt collection (for a species) from the SMP sample and dividing that by a seasonal estimate of PIT-tag detection probability. Here, detection probability, or the probability of PIT-tagged fish being detected at the dam, is believed to be equal to the probability of untagged fish entering the fish collection (or bypass) system. This is because the PIT-tag detection system is located in the bypass where detection probability is virtually 100%. The population estimates were generated for both hatchery and wild fish each year. Detection probabilities were generated from single-release mark-recapture survival estimates from releases at SMP traps above Lower Granite Dam. More details on these methods are provided below in the section titled Methods: Reach Survival Estimation using PIT-tag Mark-Recapture. SMP traps in the Salmon River, Grande Ronde River, Imnaha River and Snake River released PIT-tagged yearling Chinook and steelhead smolts above Lower Granite Dam. Seasonal detection probabilities at Lower Granite Dam from survival estimates from these trap releases were averaged over all the traps for a given species and rearing type (hatchery or wild) and then used for estimating smolt populations. 5. Methods: Summary of Mortality, Descaling, and Injury Data from SMP For this section, we summarized mortality, descaling, and injury data from the following SMP sites: Lower Granite Dam (LGR), Little Goose Dam (LGS), Lower Monumental Dam (LMN), McNary Dam (MCN), John Day Dam (JDA), Bonneville Dam (BON), and Rock Island Dam (RIS). For this report, we summarized mortality and descaling data for migration years 2003 through 2013 at all sites. This allows for a comparison of the more recent year (2013) to the previous ten years ( ). However, the injury data are only for migration years 2009 through 2013 at the FCRPS sites (i.e., all except RIS), as these are the only sites where condition monitoring occurs. Injury data are collected as part of the U.S. Army Corps of Engineers (USACE) at-project monitoring and, prior to 2009, the data collection was not standardized among hydro projects. In 2009, at the request of the Fish Passage Advisory Committee, the FPC Draft 2013 Annual Report 68 May 2014

84 coordinated with USACE to develop a standardized condition monitoring effort that assures consistency among all the hydro projects. These mortality, descaling, and injury data are used at the FCRPS projects to address possible management concerns as they occur. Sudden increases in mortality, descaling, and/or injury are generally cues that there may be a problem with the project or project operations and that management actions may be warranted. Given that these different metrics fluctuate daily, it is important to note that focusing solely on annual estimates is not sufficient to adequately describe what was seen in a particular year. a. Mortality Mortalities are generally broken into two different categories: sample mortalities and facility mortalities. At all sites, sample mortalities are those fish that are dead in the sampling tank or GBT fish that die after being sampled at the separator. These mortalities include fish that died prior to being diverted to the sample and that died as a part of the sampling process. Facility mortalities are generally quantified only at the transportation sites (LGR, LGS, LMN, and MCN). Facility mortalities are fish that are found dead in the holding raceways after having passed through the bypass system. This mortality may occur after the sample gate and, therefore, not all facility mortalities at transportation sites are represented in the sample. Consequently, estimating mortality at transportation sites presents a dilemma since using the sum of sample and facility mortalities may overestimate the mortality rate, while using the sample mortality alone may underestimate the at-project mortality. Prior to 2008, SMP personnel at JDA and BON distinguished mortalities in the sample tank as facility mortalities or sample mortalities. Facility mortalities were designated as those that were already dead before entering the sample tank. Sample mortalities were only those fish that were killed during the sampling process. Since 2008, the distinction between the two types of mortalities was dropped and all mortalities recovered in the sample tank at JDA and BON have been recorded as sample mortalities. For the transportation sites, daily mortality estimates presented in this section are based on sample mortalities divided by the daily sample. For JDA and BON, daily mortality was estimated by dividing the sum of the sample and facility mortalities by the sample count for each species. When summarizing the daily mortality data, we included days only where a minimum of 20 individuals were sampled. This was done in order to remove days with low sample sizes and, thus, potentially inflated mortality rates. For salmonids, daily mortality estimates were weighted, based on the daily passage index. Weighting for lamprey juveniles was based on the estimate of Draft 2013 Annual Report 69 May 2014

85 daily collection. This weighting allowed us to estimate a weighted average mortality for each migration year. A weighted average mortality is a more fair representation of the overall seasonal mortality, as it gives more weight to the days where a higher number of juveniles passed, versus giving equal weight to all days. b. Descaling Examinations for descaling follow the original Fish Transportation Oversight Team (FTOT) protocol established in the 1980s, where a fish is recorded as descaled if at least 20% of the scales is missing on either side. Descaling is defined as areas of the fish where scales have been removed by mechanical or other means (including predators) and scales have not regenerated or healed sufficiently. For this report, we summarized the last 11 years ( ) of descaling data at LGR, LGS, LMN, MCN, JDA, BON, and RIS for yearling Chinook, subyearling Chinook, steelhead, coho, and sockeye. Chinook and coho fry were not included in these analyses, nor were those fish that are examined for gas bubble trauma. When summarizing descaling data, we included days only where a minimum of 20 individuals were examined for descaling. This was done in order to remove days with low sample sizes and, thus, potentially inflated descaling rates. Daily descaling estimates were then weighted, based on the daily passage index. This weighting allowed us to estimate a weighted average descaling rate for each migration year. A weighted average descaling rate is a more fair representation of the overall annual descaling, as it gives more weight to the days where a higher number of juveniles passed, versus giving equal weight to all days. c. Injury SMP sites have been collecting and reporting standardized condition data to the FPC since In general, the target for condition monitoring is to collect detailed condition data on a subsample of each species that enters the sample each day (or every other day at some sites). In general, the target for these subsamples is approximately 100 individuals of each species per day. There are several physical injuries that are included in this monitoring, including: (1) head injuries, (2) eye injuries, (3) operculum injuries, (4) body injuries, and (5) fin injuries. When assessing physical injuries, SMP personnel record only injuries that are not attributable to predators, disease, or parasites. Injuries that are attributable to predators, disease, or parasites are recorded in a separate category. For this section, we summarized the last 5 years of injury data at each of LGR, LGS, LMN, MCN, JDA, and BON for salmonids only (i.e., yearling Chinook, subyearling Chinook, steelhead, coho, and sockeye). When summarizing injury data, we included days only when a minimum of 20 individuals were examined for injuries. This was done in order to remove days with low sample sizes and, thus, potentially inflated injury rates. Draft 2013 Annual Report 70 May 2014

86 To avoid double-counting, fish that exhibited multiple signs of injury were counted as a single injured fish. For salmonids, daily estimates of injury rate were then weighted, based on the daily passage index. This weighting allowed us to estimate a weighted average injury rate for each migration year. A weighted average injury rate is a more fair representation of the overall annual injury rate, as it gives more weight to the days where a higher number of juveniles passed, versus giving equal weight to all days. 6. Methods: Reach Survival Estimation using PIT-Tag Mark-Recapture Smolt survival estimates and their associated variance estimates were produced for PITtagged juvenile salmon that migrated through the river reaches between Lower Granite and Bonneville dams. PIT-tagged smolts can be detected at Lower Granite, Little Goose, Lower Monumental, McNary, John Day, and Bonneville Dams, as well as downstream of Bonneville Dam using specialized trawl equipment for PIT-tag detection. Using recapture data from fish detected at these sites, single-release mark-recapture survival estimates were generated using the Cormack-Jolly-Seber (CJS) methodology as described by Burnham et al. (1987) with the Mark program (software available free from Colorado State University) (White and Burnham 1999). When survivals from multiple reaches were combined (e.g., LGR to MCN combines 3 reaches: LGR to LGS, LGS to LMN, and LMN to MCN), variance estimates for the overall reach (LGR to MCN) were generated using the delta method (Burnham et al. 1987). The SMP calculates release to hydrosystem dam survivals for several groups of fish marked by SMP personnel (e.g., SMP traps to LMN, RIS to MCN, and hatchery releases to LGR or to MCN). In these release-to-hydrosystem dam survivals fish marked at traps, at RIS, or at hatcheries are assigned mark-recapture histories based on release and subsequent detection at some or all of the dams listed above. In most cases, survival cohorts for given species and location are formed from all fish released in a given year. However, estimates from RIS to MCN are estimated based on cohorts from shorter time intervals (2 weeks typically) so that multiple cohorts could be analyzed each year. Reach survivals (LGR to MCN and MCN to BON) create cohorts from fish detected at the upstream dam over short time intervals (1 to 2 weeks depending on species) so that multiple cohorts can be analyzed each year (1 to 8 depending on the species). Both types of estimates are presented in this report. All use single release CJS methods to estimate reach survival. 7. Methods: Estimation of Fish Travel Time Fish travel time was calculated for each survival cohort based on PIT-tag detection at dams within a reach. Travel times in this report are for the full reach from either release or detection at Draft 2013 Annual Report 71 May 2014

87 an upstream site, to the final dam in the reach. For each cohort median fish travel time was calculated based on all individuals within the cohort that were detected at both the upstream and downstream sites. These data are reported in tables and figures in the sections below and in Appendix H. 8. Methods: Environmental Variables Assigned to Survival Cohorts Spill, water transit time (WTT) and average water temperature indices were calculated for survival cohorts based on timing and fish travel time through reaches. The median fish travel time between dams for each survival cohort was used to determine the period over which to calculate the average spill, average temperature, and average WTT indices. Conditions at each dam and/or reservoir were averaged over the number of days in each cohort (unless otherwise specified in the text), and travel time to the next dam was used to adjust the start date of the calculations at that site. If there were multiple sites, as in reach survivals, then environmental variables among dams were combined for the overall reach variable. WTT is a measure of the number of days it takes an average water particle to transit the length of a reservoir. It is inversely related to average water velocity and is calculated by dividing a reservoir volume by the outflow rate. For reach survival cohorts in this report, the WTT for each cohort was the sum of the WTT for each reservoir in the reach. Average spill percentage is the percentage of the total river flow that is directed over dam spillways as opposed to through turbine units. For reach survival cohorts the overall spill percentage is the average spill percentages at each dam in the reach during cohort passage. Average temperature ( C) was measured at tail-water TDGS monitors at all dams. For reach survival cohorts the overall value reported would be the average for all monitors in that reach during passage. 9. Methods: Relative Migration Rate Relative migration rate is an indication of the fish migration rate relative to water velocity, and is useful in illustrating whether fish are travelling faster, slower, or at the same rate as the water velocity. The relative migration rate is calculated by dividing fish migration rate (kilometers/day) by the water velocity (kilometers/day). Fish migration rate is calculated by dividing median fish travel time (FTT) for a survival cohort, expressed in days, into the total distance (kilometers) in the reach resulting in an estimate of fish velocity. Similarly, water velocity would be calculated from WTT in the reach expressed in days divided into total distance. For example, the length of the reach from LGR to MCN is 225 kilometers. For a given steelhead cohort, median FTT was 10.8 (days) and WTT was 9.8 (days), so that fish velocity was 23.7 Km/day and water velocity was 25.9 Km/day. For this cohort, relative migration rate was Draft 2013 Annual Report 72 May 2014

88 23.7/25.9 or In this case the steelhead relative migration rate was less than one, indicating that fish swam through the reach slower than the velocity of water on average. Any value greater than one indicates the fish were moving faster than the average water velocity. E. Results: Collection Estimates, Relative Abundance and Population Indices 1. Snake River The Salmon River (at Whitebird, Idaho) and the Snake River (at Lewiston, Idaho) traps have included separate counts of unclipped yearling Chinook with a coded-wire tag (CWT) and counts of unclipped yearling Chinook. In addition, information was recorded in the SMP data system on holdover fall Chinook collected at Snake and Lower Columbia River sites. Holdover fall Chinook were differentiated based on morphology and timing. Specifically, yearling Chinook seen at the sites in April, exhibiting a deeply forked tail, very little descaling or fin erosion, and eye orientation consistent with fall Chinook were considered holdover yearling fall Chinook. Within the database, the code HO was used in the special species category to indicate these fish. For steelhead, fin erosion typical of a hatchery fish was also used to distinguish additional hatchery fish at the Salmon and Snake River traps. Fin erosion of steelhead has also been incorporated into sampling data at all SMP sampling dams in the Snake River as well as sites in the Columbia River. At the traps, these data were necessary in order to provide valid PIT-tag codes for PTAGIS and could be used to differentiate wild and hatchery yearling Chinook and steelhead smolts for travel time and survival estimates and to assist FPC in providing greater differentiation of hatchery fish from wild. We reported information on two categories of fish: hatchery and unmarked. The unmarked category includes fish that may be either wild or of hatchery origin, but cannot be distinguished. Rearing types are combined in this report. More detailed information can be found in appendices to the report as well as via queries on the FPC web page. Sockeye data are also presented in this report at the combined hatchery and wild level. Total collection counts at SMP traps in the Snake River basin are summarized for 2013 in Table 4.3. Trap collections are a function of the magnitude of the fish population migrating during collections as well as trap efficiency. Trap efficiency at SMP traps is known to be relatively low since SMP traps in the Grande Ronde, Salmon, and Snake rivers are situated in large rivers. Comparisons of current year collections to previous years are to provide a context for the numbers and should not be used as measures of abundance of smolts for that year. Draft 2013 Annual Report 73 May 2014

89 Table 4.3. Collection counts of composite wild/hatchery Chinook, steelhead, coho, and sockeye at the four traps used in the Smolt Monitoring Program in Species No. of Fish Sampled Species No. of Fish Sampled Salmon River Trap (above Whitebird) Snake River Trap (at Lewiston) Chinook Age 0 2 Chinook Age 0 2,668 Chinook Age 1 56,632 Chinook Age 1 2,797 Coho 0 Coho 107 Sockeye 1 Sockeye/kokanee 326 Steelhead 3,789 Steelhead 9,925 Pacific lamprey ammocoetes 0 Pacific lamprey ammocoetes 0 Pacific lamprey macropthalmia 0 Pacific lamprey macropthalmia 0 Brooke lamprey ammocoetes 0 Brooke lamprey ammocoetes 0 Imnaha River Trap Grande Ronde River Trap Chinook Age 0 61 Chinook Age Chinook Age 1 55,648 Chinook Age 1 26,301 Steelhead 40,840 Steelhead 3,547 Pacific lamprey ammocoetes 6 Pacific lamprey ammocoetes 0 Pacific lamprey macropthalmia 2 Pacific lamprey macropthalmia 0 Brooke lamprey ammocoetes 0 Brooke lamprey ammocoetes 0 The 2013 collection total for yearling spring/summer Chinook at the Salmon River trap was much higher than the current 10-year average. Over the past 10 years, the Salmon River Trap collected an average of nearly 42,000 yearling spring/summer Chinook. For steelhead, the 2013 collection total at the Salmon River Trap was also higher than the current 10-year average of approximately 2,850 steelhead smolts. Very few sockeye smolts were collected at the Salmon River trap in This is likely due to the high debris levels that caused the trap to stop collecting fish earlier than anticipated in Typically, sampling at the Salmon River trap runs through late May. However, the high flows and associated debris led to the termination of sampling on May 8, Finally, no larval or juvenile lamprey were collected at the Salmon River Trap in The yearling Chinook collection total for the Grande Ronde trap in 2013 was 26,301, which was much higher than the current 10-year average of approximately 16,000. The 2013 collection total for steelhead at the Grande Ronde trap was 3,547, which is about 81% of the current 10- year average of approximately 4,400. Subyearling Chinook collections in 2013 were much higher than more recent years. This was largely due to earlier than expected releases of hatchery subyearling fall Chinook in the Grande Ronde River. In fact, sampling at the Grande Ronde River trap was terminated on May 22 nd due to an expected release of hatchery subyearling fall Chinook upstream of the trap. Since becoming target species in 2011, no larval or juvenile lamprey have been collected at the Grande Ronde River Trap. The 2013 collection total for yearling Chinook at the Snake River Trap was 2,797. This collection total was much smaller than the current 10-year average of 11,750 yearling Chinook Draft 2013 Annual Report 74 May 2014

90 smolts. The total steelhead collection in 2013 was 9,925, which was above the current 10-year average of approximately 6,820. The total sockeye collection for 2013 was 326. As with the Grande Ronde trap, collections of subyearling Chinook at the Snake River trap were much higher in 2013 than previous years. This is largely due to earlier than expected releases of hatchery subyearling fall Chinook above the trap. In fact, due to large releases of hatchery subyearling fall Chinook that were scheduled for May 17 th, sampling from the Snake River trap was terminated on May 15 th. Finally, since becoming target species in 2011, no larval or juvenile lamprey have been collected at the Snake River trap. A summary of sample counts, collection estimates, and passage indices at Snake River collector dams is provided in Table 4.4. In 2013, a study was conducted at Lower Granite Dam to evaluate the prototype juvenile fish collection channel overflow weir and enlarged orifice. This study involved PIT-tagging clipped yearling Chinook, clipped steelhead, and clipped subyearling Chinook that were sampled as part of the SMP sample at LGR. Study fish were held overnight, PIT-tagged, and released the second day after collection into gatewell 5A, 5B, or directly into the orifice gallery channel. Occasionally, these PIT-tagged study fish were later detected re-entering the sample tank, which would result in these fish being resampled by the SMP crew. The resampling of these PIT-tagged study fish inflates the daily collection estimates and, therefore, the daily estimates of passage and population indices. In November 2013, the FPC reviewed the PIT-tag detections of these study fish at the LGR sample tank in order to investigate to what degree the resampling of PIT-tagged study fish biased collection and passage index estimates and timing (see FPC memo from Nov. 19, 2013). Based on these analyses, the FPC found that the impact on collections and passage indices were small and did not warrant a correction, particularly since the passage index is not intended to be used as a measure of population size. Furthermore, the resampling of PIT-tagged fish had no impact on the estimation of timing at LGR, when based on the passage index. After discussions with the Fish Passage Advisory Committee (FPAC), it was determined that the 2013 database for LGR would remain as-is, with no corrections applied. Collection estimates were highest for yearling Chinook at Lower Granite Dam in 2013 while steelhead had the highest collection estimates at Little Goose and Lower Monumental dams. As in recent years, yearling Chinook and steelhead dominated the collections at LGR, LGS, and LMN. Subyearling Chinook continued to have the third highest estimates of collection at all the Snake River sites. The collection totals for subyearling Chinook at LGR, LGS, and LMN were about 494,000, 453,000, and 170,000, respectively. The above-mentioned study at LGR also involved PIT-tagging and releasing Pacific macropthalmia into the gatewells and/or Draft 2013 Annual Report 75 May 2014

91 orifice gallery channel. These PIT-tagged lamprey confirmed the suspicion that juvenile lamprey are able to escape the sample tank at LGR prior to being sampled (see FPC memo from Dec. 3, 2013, for a brief overview of these findings). After escapement was confirmed, it was decided by FPAC that FPC would no longer report collection counts for larval and juvenile lamprey at LGR. Instead, only sample counts would be reported for this site until escapement is remedied. Pacific lamprey macropthalmia dominated the samples and collections at all three Snake River sites in The total collection for yearling Chinook and steelhead at the Snake River collector dams were approximately 3.4 and 3.1 million, respectively. Of the yearling Chinook and steelhead collected at the Snake River collector dams, approximately 32% 48% were transported (See Appendix G). Table 4.4. Comparison of sample, collection estimates, and passage indices of salmonids and larval and juvenile lamprey at Snake River dams in 2013 with recent annual passage indices Dam Species Sample Collection Passage Index or Collection 1 Passage Index or Collection 1 Passage Index or Collection 1 Passage Index Lower Chinook Age 0 59, , ,072 1,081,249 1,177,374 1,043,849 Granite Chinook Age 1 22,505 1,865,260 2,607,222 4,042,722 3,831,112 2,452,574 Coho ,078 61,827 69,833 83,949 40,188 Sockeye/kokanee ,772 54,819 43, ,436 8,836 Steelhead 18,698 1,444,903 2,037,075 3,538,995 4,118,595 2,045,806 Pacific lamprey ammocoetes 2 15 N/A N/A N/A Pacific lamprey macropthalmia 4 73 N/A N/A N/A Little Goose 3 Chinook Age 0 53, , ,941 1,053,282 1,365,072 1,310,588 Chinook Age 1 6,981 1,026,201 1,497,846 2,265,589 2,525,290 1,260,436 Coho ,889 54,082 78,641 81,898 53,920 Sockeye/kokanee ,634 33,025 37,272 44,351 12,833 Steelhead 10,032 1,174,684 1,713,520 1,490,314 2,032,151 1,594,144 Pacific lamprey ammocoetes N/A 1,903 6,584 N/A Pacific lamprey macropthalmia 1,279 55,077 N/A 4,749 11,108 N/A Lower Chinook Age 0 34, , , , , ,997 Monumental 4 Chinook Age 1 6, , , ,272 1,236, ,065 Coho 204 8,000 10,584 19,948 19,964 13,600 Sockeye/kokanee 156 8,064 11,380 18,240 31,278 2,202 Steelhead 7, , , , , ,909 Pacific lamprey ammocoetes 1 1 N/A 69 1 N/A Pacific lamprey macropthalmia 79 63,728 N/A 2, N/A 1 Passage Index is displayed for salmonid species (all four years) while collections are displayed for lamprey juveniles ( ). 2 Due to confirmed escapement of larval and juvenile lamprey at LGR, estimation of collection counts at are biased. Therefore, upon FPAC recommendation we report only total sample counts at this site until escapement is remedied. 3 Full Index sampling (i.e., 24-hour sub-sample to estimate collection) at Little Goose Dam began May 3, Full Index sampling (i.e., 24-hour sub-sample to estimate collection) at Lower Mon. Dam began on May 7, Draft 2013 Annual Report 76 May 2014

92 Tables 4.5 to 4.8 compare passage indices, population indices, and population estimates for yearling Chinook and steelhead at LGR in recent years. Based on the population estimate and cumulative population index, hatchery yearling Chinook passage numbers were lower in 2013 than 4 of the past 5 years (Table 4.5). Similarly, the population estimate for wild and unmarked yearling Chinook was estimated to be lower than all but the earliest 2 years (2007 and 2008), while the population index for wild Chinook was lower than 4 of the past 6 years (Table 4.6). Table 4.5. Hatchery yearling Chinook population estimates and indices at Lower Granite Dam in 2013 compared to recent years. Year Collection Efficiency Collection Estimate Passage Index Population Estimate Population Index ,554,702 2,176,594 6,030,067 6,431, ,036,472 3,073,769 7,304,960 11,075, ,251,395 3,153,250 6,640,000 8,570, ,303,790 1,977,910 7,792,000 6,072, ,981,492 2,592,000 6,190,000 7,480, ,066,898 3,076,000 5,590,000 7,790, ,331,536 1,878,000 5,330,000 5,610,000 Table 4.6. Wild and unmarked yearling Chinook population estimates and indices at Lower Granite Dam in 2013 compared to recent years. Year Collection Efficiency Collection Estimate Passage Index Population Estimate Population Index , , ,172 1,298, , ,882 1,715,148 3,591, , ,862 1,121,000 1,960, , ,657 1,235,000 1,394, , , ,000 1,490, , , ,000 1,280, , , ,000 1,240,000 Table 4.7. Hatchery steelhead population estimates and indices at Lower Granite Dam in 2013 compared to recent years. Year Collection Efficiency Collection Estimate Passage Index Population Estimate Population Index ,175,791 1,677,936 6,419,019 5,310, ,746,004 2,633,381 4,557,582 4,759, ,366,042 3,588,309 6,231,000 8,450, ,139,565 1,718,954 6,005,000 5,092, ,032,390 3,983,000 6,890,000 11,230, ,879,469 2,979,000 6,710,000 9,180, ,172,247 1,595,000 5,330,000 6,420,000 Table 4.8. Wild and unmarked hatchery steelhead population estimates and indices at Lower Granite Dam in 2013 compared to recent years. Year Collection Efficiency Collection Estimate Passage Index Population Estimate Population Index , ,286 1,098, , , ,412 1,766, , , , ,213 1,106, , , ,000 1,026, , , ,000 1,360, , , ,000 1,280, , , ,000 1,060,000 Draft 2013 Annual Report 77 May 2014

93 For hatchery steelhead the estimated population was 6.4 million, which is relatively high compared to recent years. Only the estimates for 2008 and 2009 were higher (Table 4.7). But the population index data does not agree very closely with the population estimate and shows 2013 as an average to low year. For wild and unmarked steelhead the population estimate is lower than 2012 but otherwise higher than all other recent years (Table 4.8). As with hatchery steelhead the population index, the population index for wild steelhead shows a nearly opposite relationship with the 2013 population estimate which was only higher than 2012 and lower than all other recent years. 2. Columbia River A summary of sample counts, collection estimates, and passage indices at Mid-Columbia and Lower Columbia River collector dams are provided in Table 4.9. While passage indices are best viewed as a single season measure of the daily smolt numbers, at a project such as Rock Island Dam where spill proportion and powerhouse discharge proportions have stayed relatively constant over the years, the passage index may be viewed as a relative measure of run size from year to year. However, due to the unknown collection efficiency at this project, comparisons of the passage indices at Rock Island Dam to those at other dams are not advisable, since biases associated with the unique collection system at Rock Island Dam are unknown. Based on the passage index, coho juveniles were the dominant salmonid species at Rock Island Dam in The 2012 passage index for coho juveniles in 2013 was nearly 50,000, which was slightly higher than the passage indices for this species over each of the last 3 years. In all, coho juveniles made up approximately 36% of the total passage index for salmonid species, which is within the range of the most recent 3 years (range: 29.5% in 2012 and 40% in 2010). Based on the passage index, yearling Chinook were the second most abundant species of salmonid at Rock Island Dam in The 2013 passage index total for yearling Chinook was nearly 28,315, which was higher than the passage indices of each of the last 3 years. The 2013 passage index totals for subyearling Chinook and steelhead at Rock Island Dam were lower than their respective passage indices over the last 3 years. Total sockeye passage in 2013 was lower than the 2012 passage total but within the range of what has been seen in the most recent 3 years. Finally, as was the case in 2011 and 2012, Pacific lamprey macropthalmia were the dominate life-stage for lamprey at Rock Island Dam. Draft 2013 Annual Report 78 May 2014

94 Table 4.9. Sample, collection, and passage indices of salmonids and larval and juvenile lamprey at Columbia River dams in 2013and comparison with 2010 to 2012 annual passage indices. Dam Rock Island Dam Passage Index or Collection a Passage Index or Collection a 2011 Passage Index or Collection a 2010 Passage Index Species Sample Collection Chinook Age 0 11,677 11,677 18,794 28,725 31,133 23,362 Chinook Age 1 17,059 17,059 28,315 25,797 26,463 11,800 Coho 28,981 28,981 49,973 49,618 46,400 41,441 Sockeye/kokanee 14,590 14,590 25,107 46,856 18,763 36,508 Steelhead 8,891 8,891 14,984 17,329 28,473 17,309 Pacific lamprey 9 9 N/A 8 54 N/A ammocoete Unknown lamprey ammocoete 0 0 N/A 1 1 N/A Pacific lamprey macropthalmia N/A N/A McNary Dam b Chinook Age 0 54,878 3,563,684 7,405,326 6,207,586 8,426,605 6,936,373 Chinook Age 1 19,763 2,195,928 4,243,159 4,357,822 3,942,360 4,186,948 Coho 1,152 87, , , , ,908 Sockeye/kokanee 4, ,872 1,267,016 2,271, ,922 2,937,029 Steelhead 4, , ,900 1,085,887 1,201, ,036 Pacific lamprey 0 0 N/A 200 1,170 N/A ammocoete Unknown lamprey ammocoete 0 0 N/A 0 30 N/A Pacific lamprey macropthalmia 2, ,398 N/A 242, ,568 N/A John Day Dam Chinook Age 0 20,374 1,653,322 2,553,455 3,974,383 3,301,558 2,240,563 Chinook Age 1 17,081 1,291,293 2,057,080 4,290,283 2,936,440 1,034,554 Coho 1, , , , , ,181 Sockeye/kokanee 2, , , , , ,084 Steelhead 5, , ,377 2,834,884 2,620, ,822 Pacific lamprey Bonneville Powerhouse 2 ammocoete N/A 12,283 28,145 N/A Pacific lamprey macropthalmia 4, ,896 N/A 490, ,333 N/A Chinook Age 0 (All) 25,888 1,849,466 4,866,372 5,584,698 5,219,966 5,118,656 Chinook Age 0 c (Brights only) 17,411 1,073,612 2,826,145 3,228,586 2,552,157 3,294,637 Chinook Age 1 12, ,940 1,881,678 2,538,937 1,322,343 2,302,148 Coho 8, , , , , ,989 Sockeye/kokanee 1, , , , , ,520 Steelhead 3, , , , , ,451 Pacific lamprey ammocoete Pacific lamprey macropthalmia N/A N/A 495 6,143 N/A 31,755 25,406 N/A a Passage Index is displayed for salmonid species (all four years) while collections are displayed for lamprey juveniles ( ). b McNary sampled every other day from April 7 to July 16 in 2010, April 13 to July 20 in 2011, April 11 to August 17 in 2012, and April 7 to September 30 in Because of these changes to sampling, passage indices were adjusted for comparison to historic data by interpolating values for dates not sampled or only partially sampled (project operated primary bypass) between two sample dates. As an example, for yearling Chinook the unadjusted passage index for 2013 was 2,121,888 compared to an adjusted passage index of 4,243,159, which is the projected passage index if every day sampling were implemented. c Up-River brights annual values were summed commencing June 1 in each of the years presented in Table 4.9 due to tule Chinook releases from hatcheries prior to that date in each year masking the patterns in outmigration magnitude and timing. Draft 2013 Annual Report 79 May 2014

95 At McNary Dam, sampling schedule and project operations have changed considerably in recent years. These changes mean that indices are not a good gauge of long-term population size as compared to Rock Island Dam. Similarly, there have been several operational changes at John Day and Bonneville dams over the years, particularly in terms of spill proportions as well as the addition of surface bypass routes at those projects. Therefore, making comparisons of indices between years and projects is less meaningful for these projects than for Rock Island Dam. Due to no transportation operations in 2013, sampling at McNary Dam in 2013 was everyother-day for the entire SMP season. This is different from what has been done in previous years when transportation has generally started in summer and continued through the end of the SMP season. Subyearling Chinook were the dominant species of salmonids at McNary, John Day, and Bonneville Dams in This pattern of higher passage indices for subyearling Chinook at these three projects is consistent with what has been observed in recent years. The one exception was in 2012 when yearling Chinook dominated the total passage index at John Day Dam. Yearling Chinook had the second highest total passage indices among the salmonid species at McNary, John Day, and Bonneville dams in Finally, Pacific lamprey macropthalmia dominated the larval and juvenile lamprey collections at all three Lower Columbia collector dams. In fact, Pacific ammocoete collections at these three sites were extremely low in 2013, when compared to recent years. F. Results: Migration Timing When compared to the current 10-year average, arrival timing (i.e., estimated 10% passage date) of most species at Lower Granite Dam was very similar in 2013 (Table 4.10). The only salmonid species whose 10% passage date in 2013 was more than 7 days different than the 10-year average was sockeye/kokanee. The estimated 10% passage date for sockeye/kokanee in 2013 was May 15 th, whereas the current 10-year average 10% passage date was May 4 th. This later arrival timing is likely due to the lack of spill at Dworshak in April, which meant that fewer/no kokanee were sampled at Lower Granite Dam in April. In general, the estimated 50% passage date for all salmonids at Lower Granite Dam for 2013 was very similar to the current 10-year average (Table 4.10). However, this was not the case for the estimated 90% passage dates. Subyearling Chinook at Lower Granite Dam had a much later 90% passage date in 2013 (July 17 th ) than the current 10-year average (July 9th) while coho and sockeye had earlier 90% passage dates in 2013 than their respective 10-year average 90% passage dates (Table 4.10). Draft 2013 Annual Report 80 May 2014

96 Table Migration timing of salmonids and larval and juvenile Pacific lamprey at Lower Granite, Rock Island, McNary, and John Day dams in 2013 compared to 2012 and 2011 and the 10-year average ( ). Dam Lower Granite Rock Island 2013 Percent passage 2012 Percent passage 2011 Percent passage 10 Year Average Percent passage Species Chinook Age 0 5/30 6/9 7/27 5/30 6/14 7/12 5/26 6/10 7/14 5/30 6/11 7/9 Chinook Age 1 4/19 5/8 5/14 4/16 4/27 5/16 4/18 5/8 5/17 4/20 5/4 5/16 Coho 5/8 5/14 5/18 4/28 5/17 5/26 5/6 5/17 6/2 5/6 5/18 5/31 Sockeye and kokanee 5/15 5/17 5/19 5/5 5/19 5/26 4/4 5/21 6/5 5/4 5/21 6/2 Steelhead 4/19 5/9 5/17 4/16 4/28 5/20 4/3 5/10 5/25 4/22 5/8 5/24 Pacific macrop. b 4/12 7/13 10/6 3/29 4/5 9/26 4/2 4/17 10/2 N/A N/A N/A Pacific ammo. b 5/22 7/17 10/2 4/3 6/25 8/23 7/5 7/13 7/25 N/A N/A N/A Chinook Age 0 6/3 7/9 8/3 6/10 7/12 8/4 5/29 7/7 8/1 5/17 6/8 6/27 Chinook Age 1 4/30 5/14 5/29 4/22 5/7 5/20 4/27 5/13 5/27 4/25 5/11 5/29 Coho 5/11 5/20 5/30 5/9 5/16 5/31 5/16 5/27 6/6 5/15 5/24 6/5 Sockeye 5/10 5/16 5/20 4/30 5/9 5/18 5/6 5/20 6/13 4/29 5/17 6/2 Steelhead 5/9 5/16 5/29 4/29 5/10 5/30 5/13 5/23 6/15 5/6 5/18 6/3 Pacific macrop. b 4/11 6/27 8/13 4/10 4/29 7/30 4/10 4/29 7/30 N/A N/A N/A Pacific ammo. b 4/7 5/16 7/5 4/18 5/1 8/28 4/30 5/18 7/21 N/A N/A N/A McNary Chinook Age 0 6/17 7/5 7/22 6/21 7/12 8/14 6/8 7/13 8/4 6/15 7/3 7/22 Chinook Age 1 5/1 5/10 5/28 4/29 5/9 5/24 4/29 5/10 5/26 4/29 5/12 5/26 Coho 5/4 5/21 6/7 5/6 5/22 6/4 4/28 5/24 6/9 5/10 5/25 6/8 Sockeye 4/30 5/16 5/25 5/1 5/11 5/21 5/5 5/18 6/2 5/8 5/20 6/1 Steelhead 4/24 5/5 5/22 4/22 5/2 5/19 4/21 5/6 5/25 4/25 5/10 5/26 Pacific macrop. b 5/15 5/25 8/20 5/2 5/18 7/10 4/23 5/24 6/17 N/A N/A N/A Pacific ammo. b N/A N/A N/A 7/3 7/4 7/5 5/21 6/20 7/10 N/A N/A N/A Bonneville Chinook Age 0 PH 2 a Brights 6/27 7/9 7/16 6/23 7/9 7/26 6/23 7/13 8/1 6/18 7/3 7/20 Chinook Age 1 4/28 5/12 5/21 4/24 5/12 5/23 4/17 5/10 5/18 4/20 5/10 5/25 Coho 4/16 5/14 6/1 4/25 5/18 6/7 4/11 5/14 5/24 4/24 5/14 5/31 Sockeye 5/14 5/20 5/26 5/9 5/14 5/23 5/4 5/17 6/4 5/12 5/22 6/3 Steelhead 4/28 5/10 5/31 4/28 5/10 5/28 4/24 5/13 5/30 4/30 5/14 5/30 Pacific macrop. b 3/24 6/3 7/16 3/22 4/14 6/22 3/25 4/15 5/29 N/A N/A N/A Pacific ammo. b 3/22 5/29 7/20 3/29 4/14 8/3 4/9 5/28 7/31 N/A N/A N/A a Annual values for Chinook Age 0 Brights are summed commencing June 1 since tule Chinook releases from Spring Creek NFH and Little White Salmon NFH have occurred in March, mid-april, and/or early May over the past 10 years. b Migration timing of larval and juvenile Pacific lamprey are based on sample counts at LGR and collection counts at RIS, MCN, and BON. At Rock Island Dam, differences in arrival timing among the various salmonid species in 2013 were similar to their respective 10-year averages, with two exceptions. This is the fifth consecutive year where subyearling Chinook timing was later than the historic average. The estimated 10%, 50%, and 90% passage dates for subyearling Chinook at Rock Island Dam in 2013 were June 3 rd, July 19 th, and August 3 rd, respectively (Table 4.10). By comparison, the current 10-year average 10%, 50%, and 90% passage dates for subyearling Chinook are May 17 th, June 8 th, and June 27 th (Table 4.10). Sockeye arrival timing also appeared to be slightly later in 2013, when compared to the current 10-year average (Table 4.10). However, the 90% passage dates for sockeye at Rock Island Dam in 2013 was almost 2 weeks earlier than the respective 10-year average (Table 4.10). Draft 2013 Annual Report 81 May 2014

97 Overall, passage timing of juvenile salmonids at McNary Dam in 2013 was relatively similar to the 10-year average passage timing (Table 4.10). The largest difference in 2013 passage timing versus that 10-year average was among sockeye juveniles. The estimated 10%, 50%, and 90% passage dates for sockeye in 2013 were April 30 th, May 16 th, and May 25 th. By comparison, the current 10-year average 10%, 50%, and 90% passage dates for sockeye at McNary Dam are May 8 th, May 20 th, and June 1 st (Table 4.10). Passage timing at Bonneville Dam is to a large extent a function of hatchery releases into the Lower Columbia (below McNary Dam). This is particularly true for subyearling fall Chinook. Large releases of fall Chinook tules occur in Bonneville Pool in early April and May. These fish typically begin arriving at Bonneville Dam within 12 to 24 hours of their release. For this reason, we present passage timing only for subyearling Chinook brights, those subyearling Chinook that pass after June 1 st. Arrival timing for subyearling Chinook (brights) and yearling Chinook appeared to be later in 2013, when compared to the current 10-year average. For example, the estimated 10% passage date for subyearling Chinook brights was June 27 th, whereas that for the current 10-year average was June 18 th (Table 4.10). Coho arrival timing at Bonneville Dam appeared to be earlier in 2013, when compared to the average 10% passage date for the last 10 years. Other than the difference in arrival timing highlighted above, the passage timing of most species of salmonids in 2013 was very similar to the current 10-year average (Table 4.10). It is too early to determine whether the 2013 passage timing of pacific lamprey juveniles was earlier or later than other years, as 2013 was only the third year of the expanded lamprey sampling protocol. However, Table 4.10 provides the estimated 10%, 50%, and 90% passage dates of pacific lamprey ammocoetes and Pacific lamprey macropthalmia at Lower Granite, Rock Island, McNary, and Bonneville dams for 2011, 2012, and G. Results: Summary of Mortality, Descaling, and Injury Data from SMP 1. Mortality Results from these analyses are presented in Appendix I (Tables I.1 I.7). Overall, weighted average mortality rates at the various projects were variable among the years analyzed. For the Snake River projects, there does not seem to be a discernible pattern in the mortality rates among the years analyzed (Tables I.1 I.3), with one exception. The weighted average mortality for subyearling Chinook at Lower Monumental Dam in 2013 was much higher than any of the previous 10 years (Table I.3). There was also no discernable pattern in the mortality rates at MCN and JDA, as mortality rates in 2013 were within the range of what has been observed over Draft 2013 Annual Report 82 May 2014

98 the previous 10 years (Tables I.4 and I.5). However, at BON, mortality rates seem to have increased over the past 6 years ( ) when compared to the previous 5 years ( ) (Table I.6). This increase in mortality since 2008 is particularly evident for subyearling Chinook and sockeye and coincides with modifications that were made to the juvenile bypass system at the second powerhouse (PH2) prior to the 2008 out-migration. These modifications were made in order to improve the proportion of fish passing through the system. A study conducted by Hughes et al. (2011) obtained information on velocity measurements near the screens. Results of this USACE-funded study revealed that the approach velocities in the gatewells exceeded criteria intended to improve fish passage conditions recommended by National Marine Fisheries Service and the Washington State Department of Fish and Wildlife, particularly when PH2 was operated at the upper 1% efficiency range. The high velocities and turbulent conditions under these operations could cause impingement, impact, or descaling of juvenile salmonids before they exit through the orifice into the juvenile fish bypass channel. Operation of the turbines in PH2 at the upper end of the 1% efficiency range typically occurs during periods of high flow. Therefore, these issues are not always present, as is evident in the 2010 and 2013 estimates of weighted average mortality. Since 2008, the salmon managers have made many requests to operate the turbines in PH2 at or below the mid-range of the 1% efficiency range and spill additional water if necessary. While some of these requests have been granted, there are still occasions when the preferred mid-range operation has not been met, particularly during periods of high flows. To address these concerns in 2012, the fish managers submitted two System Operational Requests (SORs), one during the passage of subyearling Chinook tules from Spring Creek NFH in April and May and another during the passage of Snake River sockeye in late May (see SOR and SOR in Appendix J). Both of these SORs called for maintaining PH2 at the mid-range of the 1% efficiency curve and passing additional flows through the first powerhouse (PH1) and spill. Both of these SORs were only partially implemented, as PH2 operations were increased to above the mid-range of the 1% efficiency curve before additional spill was to be provided. Due to generally low numbers in the sample, the estimation of a weighted average mortality rate was not always possible for larval and juvenile lamprey at the Snake River sites (LGR, LGS, LMN) and Rock Island. However, higher sample counts at the Lower Columbia River sites (MCN, JDA, BON) have facilitated the estimation of weighted average mortality in each of the past 3 years. Over the last 3 years, the weighted average mortality of Pacific macropthalmia at MCN has ranged from 1.5% in 2013 to 5.4% in 2011 (Table I.4), which is generally higher than that for salmonids in each of these years. At JDA, the weighted average morality for Pacific Draft 2013 Annual Report 83 May 2014

99 macropthalmia has been in the same range as that for salmonids (Table I.5). Finally, the weighted average mortality for Pacific macropthalmia at BON was 8.0% in 2011, 8.9% in 2012, and 4.7% in 2013 (Table I.6). These annual estimates were much higher than what was estimated for salmonids in each of these years. 2. Descaling Results from these analyses are presented in Appendix I (Tables I.8 I.14). As with mortality rates, weighted average descaling rates at the various projects were variable between the years we analyzed. For most of the projects, there does not seem to be a discernible pattern in the descaling rates among the years, except LGS. At LGS, descaling rates seem to have decreased over the past 6 years ( ), when compared to the previous 5 years ( ) (Table I.9). In addition, sockeye juveniles at BON consistently had higher descaling rates over the 11 years we analyzed (Table I.13), when compared to other species and other sites. Finally, the average descaling for subyearling Chinook at LGR was the second highest in 2013, when compared to the previous 10 years (Table I.8). When the daily descaling rates are plotted over the entire year, it becomes clear that this high average descaling rate is largely due to higher than average descaling rates in August (Figure 4.1). This is the second year in a row with unusually high descaling of subyearling Chinook in the later portion of the season. This is just one example of why it is important to consider daily rates of descaling when evaluating management actions. Figure 4.1. Daily descaling rates of subyearling Chinook at LGR in 2013, 2012 and the 10-year average ( ). Draft 2013 Annual Report 84 May 2014

100 3. Injury Results from these analyses are presented in Appendix I (Table I.15). Weighted average injury rates were also variable between sites and years. With only 5 years of data, it is difficult to detect discernible patterns in the weighted average injury rates among the years (Table I.15). However, a couple of patterns are worth noting. First, it appears that the last 2 years (2012 and 2013) had the highest weighted average injury rates for subyearling Chinook and yearling Chinook at both LGR and LGS. Second, it appears that steelhead often had the highest weighted average injury rates, when compared to the other four species. This appears to be the case at all the FCRPS sites in most of the years analyzed (Table I.15). H. Results: Travel Time and Survival Analyses for Hatchery and Trap Releases 1. Snake River Traps Median travel times of yearling Chinook and steelhead smolts released from SMP traps between April 20 and May 20 each year were summarized in Table Based on past years monitoring, it appears that wild yearling Chinook migrated more rapidly than hatchery origin fish from release to Lower Granite Dam, when marked over the same time period. That pattern of wild Chinook having more rapid travel times continued in Flows during the index time period of April 10 to May 10 were relatively low in 2013 and yet fish travel times were near or more rapid than average for all but one of the Chinook release groups. The exception was for the hatchery Chinook released at the Salmon River Trap, which showed a relatively slower median travel time in 2013 at 20.5 days from release to LGR. Past years monitoring data also indicate that steelhead typically migrate much more rapidly than yearling Chinook released from the same traps. Yearling Chinook begin migration earlier than steelhead and arrival into the hydrosystem is earlier than for steelhead. But, differences in travel time suggest that although steelhead tend to begin migrating from tributaries later (see Appendix D Migration Timing Plots) they are able to catch up with yearling Chinook by the time those populations reach LGR. Overall, arrival timing of the two species differs by only a few days in terms of 10% and 90% passage dates at LGR (Table 4.10). In 2013 steelhead showed near average travel times compared to the long-term average (Table 4.11). Similar to Chinook, steelhead released at the Salmon River Trap had longer than average travel times. Draft 2013 Annual Report 85 May 2014

101 Table Median travel time and flow for hatchery (H) and wild (W) yearling Chinook and steelhead released from traps on the Salmon, Imnaha, Grande Ronde, and Snake rivers to Lower Granite Dam in 2013 compared to other recent years. Average 1 Median Travel time (days) 2 Year Flow (Kcfs) Salmon River Trap Imnaha River Trap Grande Ronde River Trap Snake River Trap Yearling. Chinook H W H W H W H W na Avg Steelhead H W H W H W H W Avg Flow averaged from April 20 to May 20 at Lower Granite Dam. 2 Seasonal median travel time estimates of trap PIT-tagged fish released between April 10 and May 10. Survival estimates for SMP trap releases of yearling Chinook and steelhead from release to Lower Monumental Dam are summarized in Tables 4.12 and The highest survival for yearling Chinook releases in 2013 was for wild Chinook released at the Grande Ronde trap (Table 4.12). This was likely due to the proximity of these releases to Lower Granite Dam relative to the other traps which were more distant (except for the Snake trap release of wild Chinook which is nearer to LGR and had similar if only slightly lower survival at 0.868). Similar to Chinook, the highest reach survival estimate for steelhead was for the wild steelhead released at the Grande Ronde trap, with an estimate of The estimated survival for wild steelhead released from the Salmon River trap was considered unreliable and was not reported here. Draft 2013 Annual Report 86 May 2014

102 Table Annual reach survival estimates of Snake River basin PIT-tagged yearling Chinook from trap release sites to Lower Monumental Dam tailrace for years 2008 to Tag Site Species Rearing type Year Survival Lower Limit Upper Limit Salmon River trap Chinook Hatchery Hatchery Hatchery Hatchery Hatchery Hatchery Wild Wild Wild Wild Wild Wild Snake River trap Chinook Hatchery Hatchery Hatchery Hatchery Hatchery Hatchery Wild Wild Wild Wild Wild Imnaha River trap Chinook Wild Wild Wild Wild Wild Wild Grande Ronde River trap Chinook Hatchery Hatchery Hatchery Hatchery Hatchery Hatchery Wild Wild Wild Wild Wild Wild Draft 2013 Annual Report 87 May 2014

103 Table Annual reach survival estimate of Snake River basin PIT tagged steelhead from trap release sites to Lower Monumental Dam tailrace in the years 2008 to Tag Site Species Rearing type Year Survival Lower Limit Upper Limit Salmon River trap Steelhead Hatchery Hatchery Hatchery Hatchery Hatchery Hatchery Wild Wild Wild Wild Snake River trap Steelhead Hatchery Hatchery Hatchery Hatchery Hatchery Hatchery Wild Wild Wild Wild Wild Wild Imnaha River trap Steelhead Wild Wild Wild Wild Wild Wild Grande Ronde River trap Steelhead Hatchery Hatchery Hatchery Hatchery Hatchery Hatchery Wild Wild Wild Wild Wild Wild Draft 2013 Annual Report 88 May 2014

104 2. Mid-Columbia Hatcheries Median fish travel times for Mid-Columbia PIT-tag release groups are reported in Table 4.14 while survival estimates are provided in Table Three hatchery groups were marked and released in 2012 as part of the Smolt Monitoring Program. Leavenworth National Fish Hatchery located on the Wenatchee River near Leavenworth, Washington, released 14,951 PIT-tagged yearling Spring Chinook. At Wells State Fish Hatchery (Washington) 5,963 subyearling summer Chinook were PIT-tagged and released. And at Priest Rapids State Fish Hatchery (Washington) 2,992 subyearling fall Chinook were released. Table Median travel time for Mid-Columbia River hatchery Chinook from hatchery site to McNary Dam in 2013 compared to 2010 to Flows at Priest Rapids Dam were used as an index of total discharge each year in the reaches. Hatchery Age Leavenworth 1 1 Wells (May) 1 0 Priest Rapids 2 0 Migration Year Med FTT Index Med FTT Index Med FTT Index Med FTT Index (90%CI s) Flow (90%CI s) Flow (90%CI s) Flow (90%CI s) Flow ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) Flows were calculated as a 2-week average at Priest Rapids Dam beginning at release date plus ½ the release to McNary travel time (reflecting that PRD is midpoint: 190 km of 360 total km between Wells and McNary Dam; also PRD is also a midpoint for Leavenworth NFH to McNary Dam: 160 km of the total 330 km). 2 Priest Rapids Hatchery s flows are computed as average flows over a 9- to 10-day period encompassing three releases separated 3 5 days apart (except 2013 when releases were over a 4 day period and flows were averaged from June 12 to 15). Median fish travel time in 2013 for yearling Chinook released from Leavenworth NFH was relatively long at 24.8 days, although travel times were longer in 2012 (Table 4.14). For the Wells release of subyearling summer Chinook, travel times were very slow relative to other recent years at 51.4 days. Based on a regression analysis of median fish travel time and index flow, we found no significant relations (α = 0.05) between fish travel time and index flows for the hatchery groups (Table 4.14). Index flows were 2-week average flows at Priest Rapids Dam beginning at release date plus ½ the release to McNary travel time (reflecting that PRD is the approximate midpoint: 190 km of 360 total km between Wells and McNary Dam; also PRD is midway between Leavenworth NFH and McNary Dam: 160 km of the total 330 km). The fact that we found no relation between fish travel time and flows does not mean such a relationship does not exist. In fact, based on many other analyses, we suspect there is a relationship. However, size at release may have varied from year to year and may have been an important component to travel time. For example, the Wells SFH release in 2013 averaged 72 mm in fork length at marking (fish were released 2 to 3 weeks after marking each year) whereas in 2010 and Draft 2013 Annual Report 89 May 2014

105 2011 fish average 81 mm and 80 mm respectively when marked. It is likely that different size at marking confounded the results. Wide confidence intervals due to small sample sizes made patterns in these estimates difficult to interpret. Other factors are likely affecting FTT in these hatchery release groups as well. The survival estimates for Mid-Columbia River hatchery releases are summarized in Table Survival of PIT-tagged subyearling fall Chinook from Priest Rapids Hatchery to McNary Dam was 0.67 which was near average compared to recent years. Survival for the 2012 Leavenworth yearling Chinook release was which was well above the average of the recent years which was Survival for the Wells hatchery release of subyearling summer Chinook was 0.253, which was similar to that estimated for Both years reach survivals were well below the average of recent years. Table Annual average reach survival estimates of Mid-Columbia River basin PIT-tagged yearling and subyearling hatchery Chinook from release site to McNary Dam tailrace in the years 2007 to Tag Site Species Age Year Release Date Range Survival (std error) Leavenworth NFH Chinook / (0.011) / (0.022) / (0.02) /23-4/ (0.03) /19-4/ (0.022) /17-4/ (0.02) /23-4/ (0.07) Wells SFH Chinook / (0.041) / (0.037) /12-5/17 a (0.041) / (0.039) / (0.076) / (0.04) / (0.041) Priest Rapids SFH Chinook /13-6/ (0.062) /12-6/ (0.082) /11-6/ (0.059) /11-6/ (0.068) /15-6/ (0.129) /12-6/ (0.074) /12-6/ (0.07) a Volitional release at Wells Hatchery in Draft 2013 Annual Report 90 May 2014

106 I. Results: Reach Survival Analyses 1. Introduction This section provides updated analyses of smolt survivals in three reaches. For the Lower Granite Dam to McNary Dam reach, survival estimates are updates of yearling and subyearling Chinook, steelhead, and sockeye analyses done for the Comparative Survival Study (CSS) 2013Annual Report (Tuomikoski et. al., 2013). The CSS report uses reach survival data developed for the FPC Annual Report. Also presented in this section will be survival estimates for Rock Island Dam to McNary Dam reach for yearling Chinook and steelhead and Rock Island Dam to John Day Dam for sockeye. And finally, survival estimates for the McNary Dam to Bonneville Dam reach are provided for yearling Chinook and steelhead. Estimates in all these reaches provide perspectives on the smolt migration in 2013 in context of other recent years and allow comparison of 2013 conditions to those for other years in the reaches of interest. 2. Lower Granite Dam to McNary Dam Survival estimates for hatchery yearling spring/summer Chinook were similar to the range of values seen for cohorts from other recent years (2009 to 2012) (Figure 4.2A). Survivals ranged between 0.56 and 0.91 from early passage dates at LGR to the latest dates. The pattern of seasonally increasing survival seen in 2013 was also similar to most past years, although 2013 showed a larger contrast from earliest to latest cohort than had been seen in other recent years. Water transit times were longer than average (indicating lower than average flows) for all but the final cohort in 2013 (see figure 4.2B). Spill percentages were above average for all cohorts in Fish travel times ranged widely in 2013, showing a seasonally decreasing pattern that is similar to past years (Figure 4.2E). Wild yearling Chinook survivals were near average for all cohorts except one in 2013 (Figure 4.3A). Similar to hatchery yearling Chinook, fish travel times show a decreasing pattern each year with the latest cohorts having the most rapid migration times (Figure 4.3E). Migration rates of wild yearling Chinook, fish travel time relative to water transit time, have shown a similar rate to those of hatchery yearling Chinook over the years analyzed (compare Figures 4.2F and 4.3F). Draft 2013 Annual Report 91 May 2014

107 Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T Year E Relative Fish F Year Figure 4.2. Hatchery Yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except Draft 2013 Annual Report 92 May 2014

108 Survival A Water Transit B Year Year Average Spill C Average Tem D Fish Travel T Year Year E Relative Fish Year F Year Figure 4.3. Wild Yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except For subyearling Chinook in the Lower Granite to McNary Dam reach, survivals were near but above average (although not significantly) in 2013 (Figure 4.4A). Water transit times were near the long-term average but slower than that experienced by cohorts in other recent years (Figure 4.4B). On the other hand, fish travel times were below long-term average and similar to other recent years reflecting relatively rapid fish migration through the reach, which may be attributed to improved passage due to relatively high spill percentages despite the average flows (see Figure 4.4E). Draft 2013 Annual Report 93 May 2014

109 Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T E Relative Fish F Year Year Figure 4.4. Hatchery subyearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except Steelhead survival estimates in the Lower Granite Dam to McNary Dam reach showed the opposite pattern to that of hatchery yearling Chinook in 2013 with the highest survival estimated for the earliest cohort and the lowest survival for the latest cohort (Figure 4.5A). Similar to hatchery yearling Chinook the estimates showed a wide range and estimates ranged from well above to well below the long-term average. Similar to hatchery yearling Chinook there appears to be a strong seasonality to survival estimates over the years analyzed except that the seasonal pattern is reversed as previously described for Similarly, steelhead cohorts show a seasonal decrease in fish travel time through the years, although not as consistent a pattern as seen in yearling Chinook (compare Figure 4.5E to Figure 4.2E). Steelhead relative migration rates continued their pattern of increasing in 2013 (Figure 4.5F), which is likely due to the Draft 2013 Annual Report 94 May 2014

110 implementation of the court ordered spill program as well as the development of surface passage structures at all the dams in the reach. Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T E Relative Fish F Year Year Figure 4.5. Combined hatchery and wild steelhead survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except The sockeye point estimate of survival in the Lower Granite Dam to McNary Dam reach was relatively high at 0.75 which was comparable to 2009 (Figure 4.6A). Sockeye travel time was more rapid than the long-term average for the years 1998 to 2012 (Figure 4.6B). Water transit time and spill percentage was near the long-term average for the cohort in Draft 2013 Annual Report 95 May 2014

111 Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T E Relative Fish F Year Year Figure 4.6. Hatchery sockeye survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the LGR to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except McNary Dam to Bonneville Dam Yearling Chinook point estimates of survival for 2013 were very disparate, with the earlier two cohorts showing point estimates above the time-series average, while the latest estimate was well below average (Figure 4.7A). The estimates had wide confidence intervals and the poor precision provides little confidence in the seemingly erratic point estimates. The average of the three estimates ends up near the long-term average and is perhaps the best interpretation of the data available that survival was likely near average for the season. Environmental covariates, water transit time, average spill percentage, and water temperature were all near average, while fish travel time was more rapid than the long-term average (Figure 4.7E). Draft 2013 Annual Report 96 May 2014

112 Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T Relative Fish E 0.5 F Year Year Figure 4.7. Combined hatchery and wild yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the MCN to BON reach for migration years 1999 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except For the single steelhead cohort for which survival was estimable in 2013, the point value was 0.89, which was the second highest estimate only below 2012 (Figure 4.8A). But the estimate was also relatively precise and was one of only three estimates from the data set that was significantly above the long-term average. FTT of 3.5 days was the most rapid of any cohort for the whole time-series (Figure 4.8E). Environmental conditions (average spill, water transit time, and average temperature) were near average for the cohort. The relative migration of the steelhead cohort was the most rapid for the time-series and may be due to the combination of court ordered spill and the presence of surface passage structures at John Day Dam. Draft 2013 Annual Report 97 May 2014

113 Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T Relative Fish E 0.5 F Year Year Figure 4.8. Combined hatchery and wild steelhead survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the MCN to BON reach for migration years 1999 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except Rock Island Dam to McNary Dam Reach Survival Survival estimates in this reach tend to be more variable than in other reaches due in part to low detection probability at McNary Dam, the lowest dam in the reach, and due to the fact that there are no detection sites between Rock Island and McNary Dam. Finally, lower detection probability at sites downstream of McNary Dam make estimates of detection probability at McNary more variable, also contributing to wider intervals on estimates in this reach. In 2013, survival estimates were at or above the long-term average ranging from 0.62 for the first cohort to 0.93 for the last (Figure 4.9A). Fish travel times were near average for the first cohort while the last two were below average, indicating more rapid than average travel times for those cohorts in 2013 (Figure 4.9E). Relative fish migration rates were similar to past years. The Draft 2013 Annual Report 98 May 2014

114 relative migration rates for yearling Chinook in this reach are slower than Chinook in other reaches, with the average fish migration rate 54% of water transit time compared to 91% for Snake River yearling Chinook (compare Figure 4.9F to 4.2F and 4.3F). We compared relative migration rates in the McNary Dam to Bonneville Dam reach, of Snake River origin yearling Chinook to those marked at Rock Island Dam in 2013 and found the two populations responded similarly in terms of migration rates when in the same lower river reach. Tuomikoski et al. (2013) found similar instantaneous mortality rates for these groups over the years, however survivals were lower for the RIS to MCN cohorts reflecting the longer travel time at a similar mortality rate. Interestingly, there is one less dam in the RIS to MCN reach than in the LGR to MCN reach, and the free flowing Hanford section as well. Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T Relative Fish E 0.5 F Year Year Figure 4.9. Yearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except Draft 2013 Annual Report 99 May 2014

115 Survival estimates for steelhead in the Rock Island to McNary Dam reach were near the long-term average for the 2013 cohorts (Figure 4.10A). Fish travel times were more rapid than the long-term average for 2013 (Figure 4.10E). Environmental conditions were near the longterm average, but for values for the past few years, including 2013, stand in contrast to the period of relatively lower spill from 2007 to 2011 (Figure 4.10C). Subyearling Chinook point estimates of survival in the RIS to MCN reach were above the long-term average, but the estimates were imprecise with wide confidence intervals that overlapped the average (Figure 4.11A). As with steelhead in this reach, the relative migration rates for subyearling Chinook in the RIS to MCN reach were slow relative to those for Snake River subyearling Chinook (compare Figure 4.11F to 4.4F). Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T Relative Fish E 0.5 F Year Year Figure Steelhead survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except Draft 2013 Annual Report 100 May 2014

116 Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T E Relative Fish F Year Year Figure Subyearling Chinook survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except The sockeye point estimate for survival was above the long-term average in 2013 (Figure 4.12). Water Transit Time was more rapid than average while spill proportion was near the long-term average. Average temperature data was unavailable for this group. Draft 2013 Annual Report 101 May 2014

117 Survival A Water Transit B Year Year Average Spill C Average Tem D Year Year Fish Travel T Relative Fish E 0.5 F Year Year Figure Sockeye survival (A), water transit time (days) (B), spill percentage (C), average temperature C (D), fish travel time (days) (E), and relative migration rate (F), in the RIS to MCN reach for migration years 1998 to Red circles are the 2013 observed estimates. Dashed lines indicate average value over all years except J. Overall Conclusions from SMP Chapter Flows were relatively low in the Snake River in 2013, and near average to above average in the Columbia River, which led to better than average migration conditions for migrant juvenile salmonids in the Rock Island to McNary Dam reach, but below average flow conditions in the Snake River. Tuomikoski et al. (2012) concluded in their analysis of reach survival that The instantaneous mortality rates tend to be lowest under conditions of fast water transit time (WTT) and high spill levels. In addition, mortality rates tend to increase over the migration season. We found some evidence that the increased number of dams with surface passage structures in the Draft 2013 Annual Report 102 May 2014

118 spillways may be reducing mortality rates The combination of factors that influence fish travel time and instantaneous mortality are the factors that influence survival. The reach survivals in 2013 generally reflected the conditions seen during outmigration. In general lower flows in the Snake River were offset by higher spill proportions in the reach, leading to near average survivals for most groups. In the Rock Island Dam to McNary Dam reach, where flows were near or slightly above average, nearly all survivals for all species were at or above the long-term averages. For many cohorts of Snake River yearling Chinook, subyearling Chinook, sockeye and steelhead, survivals in 2013 were generally near average for the time series 1998 to 2012, with some cohorts above the long-term average and others below. Fish travel times for the Snake River cohorts also were near average with some longer and some more rapid than the long-term average. The presence of surface spill structures at all dams in the reach likely contributed to the observed survivals, particularly for steelhead and subyearling Chinook, especially considering the average to lower than average flows most groups experienced. Similar to 2012, sockeye and subyearling Chinook survivals in the Rock Island Dam to McNary Dam reach were above the long-term average. Water transit times were more rapid than average for the sockeye and subyearling cohorts, and spill percentages were at or above average resulting in better than average migrating conditions. For yearling Chinook and steelhead in the reach, survivals were near average. In the McNary to Bonneville Dam reach flows were slightly above average for the PIT-tag cohorts as were the spill proportions these groups encountered. The estimated survivals for hatchery and wild yearling Chinook and hatchery and wild steelhead PIT-tag cohorts in the reach were mostly above the long-term average for the years 1999 to Fish travel times for all cohorts were more rapid than the long-term average as well reflecting the relatively good in-river conditions. K. Literature Cited Burnham, K. P., & Anderson, D. R. GC White, C. Brownie, and K.H. Pollock Design and analysis methods for fish survival experiments based on release recapture. American Fisheries Society Monograph, 5(5). Draft 2013 Annual Report 103 May 2014

119 FPC. November 19, Inflated collection estimates at Lower Granite Dam for clipped yearling Chinook, steelhead, and subyearling Chinook due to resampling of PIT-tagged study fish.. Fish Passage Center Memorandum. FPC. December 3, Results of 2013 lamprey monitoring. Fish Passage Center Memorandum. Ferguson, J. W., R. F. Absolon, T. J. Carlson, and B. P. Sandford Evidence of delayed mortality on juvenile pacific salmon passing through turbines at Columbia River dams. Transactions of the American Fisheries Society 135: Hughes, James S., Z. Daniel Deng, Mark A. Weiland, Jayson J. Martinez and Yong Yuan, Water Velocity Measurements on a Vertical Barrier Screen at the Bonneville Dam Second Powerhouse. Energies 4, Skalski, J.R Statistical Design for the Lower Columbia River Acoustic-Tag Investigations of Dam Passage Survival and Associated Metrics. Prepared for US Army Corps of Engineers. Tuomikoski, T., J. McCann, B. Chockley, H. Schaller, P.Wilson, S. Haeseker, J. Fryer, C. Petrosky, E. Tinus, T. Dalton, R. Ehlke and R. Lessard Comparative Survival Study (CSS) of PIT-tagged Spring/Summer/Fall Chinook, and Summer Steelhead, and Sockeye 2013 Annual Report. BPA Contract # Tuomikoski, T., J. McCann, B. Chockley, H. Schaller, S. Haeseker, J. Fryer, R. Lessard, C. Petrosky, E. Tinus, T. Dalton and R. Ehlke Comparative Survival Study (CSS) of PIT-tagged Spring/Summer Chinook and Summer Steelhead 2013 Annual Report. BPA Contract # White, Gary C., and Kenneth P. Burnham. "Program MARK: survival estimation from populations of marked animals." Bird study 46.S1 (1999): S120-S139. Draft 2013 Annual Report 104 May 2014

120 V Adult Fish Passage A. Introduction In this section, counts of adult migrating salmon, steelhead, and lamprey are reviewed and compared with the past years counts and the 10-year average counts for each project. General life history, counting methods, and variables which affect dam counts are described to provide context for the annual and historic dam counts. Adult fish encounter up to nine dams on their migration to spawning grounds in the Columbia River Basin. Nine Columbia River dams and four Snake River dams were built incorporating adult fish passage facilities. Fish passage facilities are to be operated within standards and criteria to safely and effectively pass adult fish past each dam. These standards are described in Fish Passage Plans or Habitat Conservation Plans that are required as part of the Biological Opinion set forth by NOAA Fisheries. Adult fish passage was blocked upstream at Grand Coulee Dam (completed 1942) in the Columbia River. In the Snake River Basin, adult fish passage was blocked at Brownlee (completed 1959), Oxbow (completed 1961), Hells Canyon Dam (completed 1967) and Dworshak Dam (completed 1973). Bonneville Dam at river mile is the first dam encountered in the upstream migration of salmon, steelhead, and lamprey in the Columbia Basin. Table 5.1 lists each dam, its location, owner, date of completion, whether or not it has adult passage facilities, and lists the dates when other turbine units were completed. Appendix L, page L-1 includes a map of the Columbia Basin and the location of each of the hydroelectric projects included in Table 5.1. In addition, Appendix L includes a schematic view of each project and the location of adult fishways and fishway entrances. Table 5.1. Columbia and Snake River dam completion dates location (individual project schematics in Appendix L) Dam Bonneville The Dalles River Location (River Mile) Columbia River (146.1 river mile) Columbia River (191.5 river mile) Owner/ Operator USACE Portland District USACE Portland District Other Powerhouse or Turbine Date Completed Completion Dates nd Powerhouse completed (units 1-14) 1973 (units 15-22) Yes Adult Passage Facilities Yes Draft 2013 Annual Report 105 May 2014

121 Table 5.1. (continued) Columbia and Snake River dam completion dates location Dam John Day McNary Priest Rapids Wanapum Rocky Reach Wells Chief Joseph Grand Coulee Ice Harbor Lower Monumental Little Goose Lower Granite Dworshak Hells Canyon Oxbow Brownlee River Location (River Mile) Columbia River (215.6 river mile) Columbia River (292.0 river mile) Columbia River (397.1 river mile) Columbia River (415.8 river mile) Columbia River (473.7 river mile) Columbia River (515.8 river mile) Columbia River (545.1 river mile) Columbia River (596.6 river mile) Snake River (9.7 river mile) Snake River (41.6 river mile) Snake River (70.3 river mile) Snake River (107.5 river mile) North Fork Clearwater River (1.9 river mile) Snake River (247.0 river mile) Snake River (273.0 river mile) Snake River Owner/ Operator USACE Portland District USACE Portland District Grant County PUD Grant County PUD Chelan County PUD Douglas County PUD USACE Seattle District Bureau of Reclamation USACE Walla Walla District USACE Walla Walla District USACE Walla Walla District USACE Walla Walla District USACE Walla Walla District Idaho Power Company Idaho Power Company Idaho Power Company (285.0 river mile) Willamette Willamette Portland General Electric Date Completed Other Powerhouse or Turbine Completion Dates Adult Passage Facilities 1971 Yes nd powerhouse deauthorized 1991 Yes 1961 Yes 1964 Yes 1961 (units 1-4) 1971 (additional units) Yes 1967 Yes 1961 (units 1-16) 1979 (units 17-27) No 1942 Modified in 1974, 1982 and No (units 1-3) 1976 (units 4-6) Yes 1969 (units 1-3) 1981 (units 4-6) Yes 1970 (units 1-3) 1978 (units 4-6) Yes 1975 (units 1-3) 1978 (units 4-6) Yes 1973 (units 1-3, skeleton bays 4-6) Units 5 and 6 deauthorized in 1990, unit 4 deauthorized in 1995 No 1967 No 1961 No 1959 (units 1-4) 1980 (unit 5) No 1895 Yes B. Adult Counting Procedures Each of the Federal and public utility hydroelectric projects with fish passage facilities at the Columbia and Snake River projects have at least one fish counting station that reports daily counts by species. The project operators maintain responsibility for adult fish counting at their Draft 2013 Annual Report 106 May 2014

122 projects. The U.S. Army Corps of Engineers (USACE) is responsible for fish counting at Federal projects while each public utility district is responsible for the adult fish counts at each project licensed by the Federal Energy Regulatory Commission. Adult fish counting is implemented by direct observational counting in real time or by video recording which is reviewed by count personnel at later dates. Operating agencies responsible for fish counting data determine which methods or combination of methods they use at their projects. At projects where video counting is implemented, the counting station window in the fishway is monitored by a video camera. At some later time, the tape is reviewed by counting personnel and the fish counts are recorded into a data system. At projects where direct counting is implemented, counting personnel actually observe the counting window and record fish as they pass by the fishway window. Both direct counting and video counting methods monitor the same location at the counting windows at fish ladders. Generally, the USACE uses video tape fish counts at dams from November through March. Willamette Falls uses video counts and reports adult counts year round. Grant PUD operates Priest Rapids and Wanapum Dams on the upper Columbia River. These dams have video systems, allowing for 24 hours of fish counting from April 15 through November 15. Chelan County PUD utilizes 24 hour a day video counting from April 14 to November 15 each year at Rocky Reach and Rock Island projects on the upper Columbia River. Douglas County PUD utilizes 24 hour video counting from May 1 to November 15 each year. Currently, direct fish counting begins April 1 and continues through October 31 at all eight USACE Columbia River and Snake River dams with fish passage facilities. Daily fish counts are recorded from 4:00 AM to 8:00 PM PST each day (16 hours total) by fish counting personnel directly observing fish as they pass by the counting window in the fish ladders. Count personnel count the fish passing for 50 minutes of each hour. To account for the fish that pass during the breaks (160 minutes of break each day, 16*10 minutes), they add the counts made during the day's counting periods (800 minutes of counting, 16*50 minutes), multiply the total by 1.2, round to the nearest whole fish, and present that number as the estimated daily count in each ladder. Fish passing the window in a downstream direction are recorded as a minus from the total upstream count. The direct monitoring and video monitoring dates are listed in Table 5.2. The passage periods listed in Table 5.2 for spring Chinook, summer Chinook and fall Chinook were established by regional agreement and have been in place for many decades. Although specific dates are identified there is recognition through the region that there is variable overlap between races of Chinook during the times between peak passage periods. These beginning passage dates for spring, summer and fall Chinook are not exact; they represent points between the peak passage periods, with overlap between races. Draft 2013 Annual Report 107 May 2014

123 Historically, fish counting schedules have changed from year to year and project to project. Additionally, count procedures have also changed (for example, historically at some projects during non-counting hours the fishway was closed blocking passage, while at other projects the fishway was left open and fish could pass the project during non-count hours). The USACE publishes dates when fishways are closed for maintenance in their Annual Fish Passage Report. Table 5.2 includes a column listing the Columbia and Snake River fishways outage dates. Table 5.2. Dam Bonneville The Dalles John Day McNary Ice Harbor Lower Monumental Little Goose Adult dam count monitoring dates Reporting Dates for three races of Columbia River Chinook within overall count reporting dates Spring Chinook 03/15 05/31 Summer Chinook 06/01 07/31 Fall Chinook 08/01 11/15 Spring Chinook 04/01 06/03 Summer Chinook 06/04 08/03 Fall Chinook 08/04 10/31 Spring Chinook 04/01 06/05 Summer Chinook 06/06 08/05 Fall Chinook 08/06 10/31 Spring Chinook 04/01 06/08 Summer Chinook 06/09 08/08 Fall Chinook 08/09 10/31 Spring Chinook 04/01 06/11 Summer Chinook 06/12 08/11 Fall Chinook 08/12 10/31 Spring Chinook 04/01 06/13 Summer Chinook 06/14 08/13 Fall Chinook 08/14 10/31 Spring Chinook 04/01 06/15 Summer Chinook 06/16 08/15 Fall Chinook 08/16 10/31 Video Monitoring Dates ( ) 03/01/13 03/31/13 06/15/13 09/30/13 11/01/13 02/28/14 Direct Monitoring Dates (2013) April 1, 2013 to October /15/13 09/30/13 April 1, 2013 to October /15/13 09/30/13 11/01/13 02/28/14 April 1, 2013 to October /01/13 09/30/13 April 1, 2013 to October /01/13 03/31/13 11/01/13 02/28/14 April 1, 2013 to October 2013 April 1, 2013 to October 2013 April 1, 2013 to October 2013 Dates Fishways Closed ( )* Bradford Island Fishway: 12/01/13 02/28/14 East Fish Fishway: 12/03/13 01/15/14 North Fish Fishway: 01/28/14 02/28/14 North Fish Fishway: 12/02/13 12/16/13 South Fish Fishway: 01/07/14 02/28/14 Washington Shore Fishway: 01/06/14 01/24/14 Oregon Shore Fishway: 02/03/14 02/28/14 North Shore Fishway: 02/01/14 02/ 27/14 South Shore Fishway: 01/06/14 01/30/14 North Shore Fishway: 01/02/14 01/17/14 South Shore Fishway: 01/20/14 02/28/14 01/06/14 02/28/14 Draft 2013 Annual Report 108 May 2014

124 Dam Lower Granite Priest Rapids Wanapum Rock Island Rocky Reach Wells Willamette Falls Reporting Dates for three races of Columbia River Chinook within overall count reporting dates Spring Chinook 03/01 06/17 Summer Chinook 06/18 08/17 Fall Chinook 08/18 12/15 Spring Chinook 04/15 06/13 Summer Chinook 06/14 08/13 Fall Chinook 08/14 11/15 Spring Chinook 04/15 06/13 Summer Chinook 06/14 08/13 Fall Chinook 08/14 11/15 Spring Chinook 04/15 06/17 Summer Chinook 06/18 08/17 Fall Chinook 08/18 11/15 Spring Chinook 04/15 06/19 Summer Chinook 06/20 08/19 Fall Chinook 08/20 11/15 Spring Chinook 05/01 06/28 Summer Chinook 06/29 08/28 Fall Chinook 08/29 11/15 Spring Chinook 01/01 08/15 Summer Chinook None Fall Chinook 08/16 12/31 Video Monitoring Dates ( ) 03/01/13 03/31/13 06/15/13 09/30/13 11/01/13 12/30/13 Direct Monitoring Dates (2013) April 1, 2013 to October 2013 Dates Fishways Closed ( )* 01/06/14 02/27/14 04/15/13 11/15/13 Left Bank Fishway: 11/26/13 01/13/14 Right Bank Fishway: 01/22/14 02/24/14 04/15/13 11/15/13 Right Bank Fishway: 11/29/13 01/15/14 Left Bank Fishway: 01/23/14 03/06/14 04/14/13 11/15/13 Right Bank Fishway: 12/02/13 01/31/14 Left Bank Fishway: 01/02/14 01/14/14 Middle Fishway: 01/15/14 01/31/14 04/14/13 11/15/13 01/02/14 03/01/14 05/01/13 11/15/13 West Ladder: 12/12/13 01/23/14 East Ladder: 01/29/14 02/15/14 Year round Note: Steelhead were counted throughout the counting period. Summer steelhead return to the Columbia Basin over two calendar years some over winter in reservoirs and continue their upstream migration in the spring of the following year. At times early in the year, counts of steelhead at upstream projects may be higher than counts of steelhead at downstream projects. *All Dates are approximate for planning purposes. Comparison of adult counts from year to year should consider the details of counting schedules and procedures. These details can also be found in the USACE s Annual Fish Passage Reports. In these reports, counting hours and specific procedures are documented in addition to Draft 2013 Annual Report 109 May 2014

125 daily counts at each project. These annual reports can be accessed at Table 5.2 includes the regionally agreed upon dates of return of Chinook by race. These dates are recognized as encompassing the general time period of return of each race of Chinook. There is recognition that the dates established for counting are general, not exact, and that there is overlap of the races at the beginning and end of the migration period. Other species are counted and recorded in daily counts throughout the year. Winter steelhead are counted from January 1 through March 31. Most winter steelhead population groups return to tributaries below Bonneville Dam. The general dates of January 1 through March 31 are considered the timing for winter steelhead passage at Bonneville Dam. These winter steelhead return to the Hood River and Little White Salmon River. Summer steelhead returns occur throughout the Columbia and Snake rivers and their return spans over two calendar years of dam counts with some summer steelhead that enter the river later in the year, overwintering in the reservoirs and completing their upstream migration the following spring. The USACE Annual Fish Passage Report (USACE, 2013) identifies general dates of adult passage for A-run and B-run steelhead at Bonneville Dam. The USACE identifies A-run steelhead timing at Bonneville Dam as January 1 through August 25 and B-run steelhead return timing at Bonneville Dam as August 26 through December 31. C. General Life Histories Each of the species has differences in their migration and spawning distributions which affect when and where species are counted. Salmon (Oncorhynchus spp.) and steelhead (O. mykiss) in the Columbia basin use the mainstem Columbia River for migration to and from freshwater natal areas to the Pacific Ocean, where they grow from juveniles to adults. Most of the species migrate and turn off the mainstem to spawn and incubate in their natal tributaries. However, Snake River fall Chinook, Hanford Reach fall Chinook, some populations of Lower Columbia River fall Chinook, and Columbia River chum salmon spawn and incubate redds in the mainstem itself. It is important to maintain consideration of individual life histories when considering dam count data because the counts between upstream dams are reduced as salmon and steelhead turn off of the mainstem to their natal tributaries or as they spawn in mainstem river reaches. Table 5.3 summarizes the general life history of Columbia River salmon and steelhead. This table summarizes life history information from the NOAA Fisheries Biological Recovery Team Technical Papers. The geographic range of each species is shown on Maps 5.1 through 5.7. Draft 2013 Annual Report 110 May 2014

126 Table 5.3. Species Spring Chinook Summer Chinook Fall Chinook Columbia River Salmon and Steelhead Populations Upstream of Bonneville Dam Freshwater Residence Downstream Migration Age at Return 1 + years March-May 2-3 yrs. in ocean. Return as 4 5 yrs. Jacks 3 years. 1+years April-May Adults 2-3 years in the ocean; return as 4-5 year old. < 1 year 2 May-Oct Adults 2-5 yrs. Coho 1 year plus April-May 3-4 yrs. Jacks 2 yrs. Sockeye 1, 2 or 3 yrs. May 1, 2, or 3 yrs. in the ocean Winter 2 yrs. natural May 4 yrs. Steelhead 3 (2 ocean) Summer Steelhead 4 A-run B-run Pink Salmon Chum Salmon 2 yrs. natural 1 yr. hatchery 2 yrs. natural 1 yr. hatchery < 1 yr. Outmigrate in their first spring. < 1 yr. Outmigrate in their first spring. April-May 4 yrs. (2 ocean) Return to the Columbia Major Tributary Spawning Areas 1 Mar-June Snake River: Clearwater, Grande Ronde, Salmon, Imnaha, Tucannon Upper Columbia: Chelan, Wenatchee, Entiat, Methow Middle Columbia: Wind, White Salmon, Klickitat, Yakima, Hood, Deschutes, John Day, Umatilla, Fifteen Mile Creek Lower Columbia: Willamette June-July Snake River Basin: Salmon River Basin Upper Columbia: Wenatchee, Methow, Okanagon, Entiat Aug-Oct Aug-Nov June-July Nov-Mar Jan-Aug Mainstem Snake River (below Hells Canyon above Lower Granite), Clearwater River, Upper Columbia mainstem, Columbia Hanford reach, Deschutes, John Day, Umatilla, Ives Island, Little White Salmon, Klickitat Lower Columbia: Willamette, Clackskanie, Kalama, Lewis, Yamhill, Clackamas Middle Columbia: Hermand Creek, Hood River, Umatilla River Upper Columbia: Yakima, Methow, Wenatchee Snake River: Potlatch, Clearwater, Selway Snake River: Pettit, Alturas, Redfish lakes Upper Columbia: Wenatchee, Okanagan Middle Columbia: Hood River, Little White Middle Columbia: Deschutes, White Salmon, Klickitat, John Day, Wind Upper Columbia: Yakima, Walla, Walla Snake River: Salmon River basin, Clearwater River basin Snake River: Clearwater River, Salmon April-May 4 yrs. Aug-Dec (2 ocean) River basins March-April 2 yrs. Aug-Oct Snake River, Upper Columbia River, Middle Columbia River April-May 2 yrs. Oct-Nov Below Bonneville Ives Island, Pierce Island, Hamilton Creek 1. Major Spawning areas illustrated on Maps Some small, late summer migrating fall Chinook, primarily from the Clearwater River, overwinter and out-migrate the following winter as yearling fall Chinook in April. 3. Winter Steelhead timing at Bonneville Dam from USACE Annual Fish Passage Operations Plan 4. A-Run and B-run Summer Steelhead passage dates from USACE Annual Fish Passage Report. Draft 2013 Annual Report 111 May 2014

127 The following Maps 5.1 through 5.7 show the spatial distribution of each species in the basin and the 2013 dam counts through the system of mainstem hydroelectric projects compared to 2012 counts and the 10-year average. Draft 2013 Annual Report 112 May 2014

128 Map 5.1. Spring Chinook spatial distribution and 2013 adult dam counts as percentages of the 2012 and 10-year average counts Draft 2013 Annual Report 113 May 2014

129 Map 5.2. Summer Chinook spatial distributions and 2013 adult dam counts as percentages of the 2012 and 10-year average counts Draft 2013 Annual Report 114 May 2014

130 Map 5.3. Fall Chinook spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Draft 2013 Annual Report 115 May 2014

131 Map 5.4. Coho spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Draft 2013 Annual Report 116 May 2014

132 Map 5.5. Sockeye spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Draft 2013 Annual Report 117 May 2014

133 Map 5.6. Snake River Sockeye spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average counts Draft 2013 Annual Report 118 May 2014

134 Map 5.7. Steelhead spatial distribution and the 2013 adult dam counts as percentages of the 2012 and 10-year average dam counts Draft 2013 Annual Report 119 May 2014

135 D. Variables Affecting Dam Counts Throughout this report, the 2013 counts are compared with both the 2012 and 10-year average counts. Comparison of dam counts is useful for considering general trends among years. However, consideration of dam counts alone does not provide an adequate assessment of the status of fish populations since dam counts reflect the cumulative effects of various management environmental and operational factors. For example, 10-year average counts include changes in the hatchery programs, project operations, and harvest management. Annual dam counts can be affected by harvest management, environmental factors (such as water temperature), project operations, and project structures. In 2008 NOAA Fisheries issued biological opinions under the auspices of the Endangered Species Act process for the Operation of the Federal Columbia River Power System (FCRPS) and concurrently issued the US v Oregon NOAA Fisheries Biological Opinion for Harvest Impacts (Harvest BiOp). Harvest of Columbia River stocks is managed according to the Harvest BiOp. The BiOp for the FCRPS has established an 85% adult upstream migration success rate as a goal for adult mainstem passage. The results of the implementation of these BiOps are reflected in resulting dam counts. Dam counts reflect these major management changes as well increases or decreases in hatchery production programs, or changes in hatchery production programs. Increases in hatchery programs can result in increased adult dam counts but could mask decreases in the adult counts of weaker stocks. Recognizing the limitations inherent in dam count data, fishery managers utilize adult dam count data in conjunction with PIT tag and coded-wire tag data, as well as scale sample data and DNA tissue sample data in their analyses of adult return data. Adult dam counts and PIT-tag detection data are used in the calculation of conversion rates and in the prediction of adult returns and assessment of adult migration success rate goals. Conversion rates are an assessment of adult upstream migration success, comparing PIT-tag detections and number of fish at a downstream project with the tag detections and numbers of fish that arrive at the upstream project. This report uses the both the direct and video monitoring counting schedules from each of the dams with adult passage facilities so that 2013 year counts can be compared with 2012 annual count data and 10-year average counts as a general comparison. Adult dam counts are comprised of returning hatchery and wild salmon. Dam counts are useful when combined with other data and consideration of individual population migration characteristics. Dam counts are the counts of fish that pass through a dam s fishway. For example, adult sockeye count disparities have been observed between McNary Dam and Priest Rapids Dam with higher adult Draft 2013 Annual Report 120 May 2014

136 counts occurring at Priest Rapids than at the downstream dam, McNary. It has been noted that some portion of sockeye salmon will lock through mainstem dams with navigation locks, therefore avoiding the fishway, the fishway counting window, and PIT-tag detectors. McNary Dam has navigation locks and Priest Rapids Dam upstream does not have navigation locks. The counts between upstream dams are reduced as salmon and steelhead turn off of the mainstem to spawn in their natal tributaries, and due to harvest, fall back, and adult mortality. As the adult salmon move through the Columbia River basin, they pass through many established fisheries. These include commercial non-indian fisheries, commercial Treaty Indian fisheries, and sport fisheries. Table 5.4 lists the fisheries, type of fisheries, the species associated with each fishery, and the approximate dates of the fisheries in 2013 (LeFleur, 2013). These fisheries and harvest rates are managed under the auspices of the NOAA Harvest BiOp within the U.S. v Oregon process. Fisheries data, catch, seasons, predictions, and actual run size are all published with the U.S. v Oregon process in annual publications entitled, Columbia River Compact Columbia River Mouth Fish Returns, Actual and Forecasts, (Jan. 2013) Table Major CRB salmonid fisheries Fishery Fishery type Species Buoy 10 Estuary sport Fall Chinook, hatchery coho fishery Columbia mouth to Mainstem Hatchery spring Chinook, Bonneville Dam sport fishery summer Chinook, fall Chinook, hatchery coho, hatchery steelhead (winter and summer) Above Bonneville to Priest Rapids Dam Columbia mouth to Bonneville Dam Select Area fisheries (SAFE)* Zone 1 All mainstem Columbia River fisheries between Bonneville Dam and McNary Dam (commonly known as Zone 6) Mainstem sport fishery Commercial fishery Commercial fishery Treaty Indian fishery Hatchery spring Chinook, summer Chinook, fall Chinook, coho, hatchery steelhead (winter and summer) Hatchery spring Chinook, summer Chinook, fall Chinook, coho Spring Chinook, fall Chinook, coho Spring Chinook, summer Chinook, fall Chinook, coho, sockeye, steelhead (winter and summer) 2013 Management Periods Fall Season (Aug 1 Dec 31) Winter-Spring Season (January 1 June 15) Summer Season (June 16 July 31) Fall Season (Aug 1 Dec 31) January 1 December 31 *SAFE fish return to terminal areas. They are released from net pens and return to areas downstream of Bonneville Dam, near the river mouth. Hydroelectric project operations, uncontrolled spill, spill patterns, powerhouse turbine unit location, turbine unit operational patterns (unit priorities), spillway operation patterns and fish Draft 2013 Annual Report 121 May 2014

137 facility operations can all affect adult passage and adult counts. Fallback behavior by Chinook salmon and steelhead has been documented at all Columbia and Snake River dams (Reischel and Bjornn 2003; Boggs et al. 2004a) and has caused extensive migration delays (Keefer et al. 2004) and decreased escapements to spawning grounds (Boggs et al. 2004b; Keefer et al. 2005). Additionally, fall-back can also increase the count at an upstream dam if fish fall back through the spillway and ascend the ladder. Factors such as river flow and water temperature affect adult migration, adult success rate, migration timing and adult counts. For example, research has shown that water temperature affects adult fish passage through hydroelectric projects. Clabough et al. (2009) studied the influence of water temperature on salmonid passage at the Lower Granite Dam fishway. Water temperatures were monitored within the LGR fish ladder concurrently with the passage of radiotagged adult salmonids at the dam. Clabough et al. (2009) found that a significantly high percentage of spring/summer Chinook salmon exited the fish ladder to the tailrace when temperatures exceeded 64.4 F compared to when water temperatures were less than 64.4 F. However, a significant percentage of the steelhead and fall Chinook did not exit the ladder to the tailrace, when temperatures were greater than 64.4 F. Overall, they reported that a higher percentage of fish remained in the ladder overnight when water temperatures were greater than 64.4 F (Clabough et al., 2009). Goniea et al. concluded that adult fall Chinook salmon migration rates slowed in the lower Columbia River when water temperatures were above 68 F. Slowed migration was strongly associated with temporary use of tributaries, which averaged 3 to 12 F cooler than the main stem (Goniea et al., 2006). In 2003 the EPA developed a guidance document for water quality standards, including temperature, titled EPA Region 10 Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards. This was developed to assist States and Tribes to adopt temperature water quality standards that EPA could approve consistent with its obligations under the Clean Water Act (CWA) and the Endangered Species Act (ESA). Consistent with the guidance document the State of Oregon developed the following administrative ruling: The seven-day-average maximum temperature of a stream identified as having a migration corridor use on subbasin maps and tables Oregon Administrative Rule (OAR) to : Tables 101B, and 121B, and Figures 151A, 170A, 300A, and 340A, may not exceed 20.0 degrees Celsius (68.0 degrees Fahrenheit). In addition, these water bodies must have cold water refugia that are sufficiently distributed so as to allow salmon and steelhead migration without significant adverse effects from higher water temperatures elsewhere in the water body. Finally, the seasonal thermal pattern in Columbia and Snake Rivers must reflect the natural seasonal thermal pattern. Draft 2013 Annual Report 122 May 2014

138 The State of Washington (Washington Department of Ecology WA-DOE) water temperature criteria is measured by the 7-day average of the daily maximum temperatures (7- DADMax) and is set at 17.5ºC (63.5ºF) for fresh water where salmonid rearing and migration occurs. The WA-DOE incorporates the following guidelines on preventing acute lethality and barriers to migration of salmonids into determinations of compliance with the narrative requirements for use protection established [e.g., WAC A-310(1), A-400(4), and A-410 (1)(c)]: Moderately acclimated (16 20 C, or F) adult and juvenile salmonids will generally be protected from acute lethality by discrete human actions maintaining the 7-DADMax temperature at or below 22 C (71.6 F) and the 1-day maximum (1-DMax) temperature at or below 23 C (73.4 F). The State of Idaho Department of Environmental Quality (ID-DEQ) disagrees with EPA over acceptable criteria for temperature for Idaho water bodies. Idaho participated in developing the EPA 2003 guidance document, but in the end dissented on most of the recommended criteria due to reservations as to their attainability. At issue for the State of Idaho is the balance between temperature that is protective of cold-water dependent species yet attainable in most water bodies. ID-DEQ's current stream temperature standards protect aquatic life uses, the only uses that have temperature requirements. The ID-DEQ current standard for cold water is a maximum daily maximum temperature of 22ºC (72ºF). Given the existing State of Washington and Oregon criteria for temperature, the general goal in the FCRPS is to not exceed the 20ºC (68ºF) in the migration corridor. For the State of Washington criteria see: Water Quality Standards for Surface Waters of the State of Washington Chapter A WAC Amended May 9, Revised January 2012, Publication no For the State of Idaho Criteria see: For the State of Oregon see: Draft 2013 Annual Report 123 May 2014

139 For EPA criteria see: U.S. Environmental Protection Agency EPA Region 10 Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards. EPA 910-B Region 10 Office of Water, Seattle, WA. When comparing dam counts to other dam counts, it is important to consider the spatial and temporal changes in counts due to mortality; spawning timing; and tributary and hatchery turn offs; harvest; changes in hatchery programs; and the differences in how each of the agencies count adults. Environmental conditions such as flow, spill, and water temperature differences in each year should be considered when comparing dam counts. This being noted, dam counts in the region illustrate the regional spatial distribution of each species and the general difference in populations that move into each of the major watershed production areas, as we have done in this report. E Passage Conditions 1. Water Temperature Water temperature is monitored at the forebay and tailrace of each federal hydroelectric project in conjunction with the USACE Dissolved Gas Monitoring Program for compliance with the state water quality standards. Gauges are installed, calibrated, and maintained by the USACE. The gauges collect water temperature data, barometric pressure, total dissolved gas, and gauge depth on an hourly basis with the data transmitted every 4 hours electronically. The USACE posts the data on their website (USACE, 2012). Figures 5.1a through 5.1e graph the 2013 water temperatures in the forebay and tailwater for Bonneville, McNary, Priest Rapids, Rock Island, and Lower Granite Dams collected as a component of the USACE Dissolved Gas Monitoring Program. Based upon the water quality criteria of 68ºF, a temperature which can be problematic for adult passage and survival, Table 5.5 lists the number of days and times when the water temperature was over 68ºF in the forebays and tailwaters at specific dams. Draft 2013 Annual Report 124 May 2014

140 Figure 5.1a Bonneville Dam average daily water temperature Figure 5.1b McNary Dam average daily water temperature Draft 2013 Annual Report 125 May 2014

141 Figure 5.1c Lower Granite Dam average daily water temperature Figure 5.1d Priest Rapids Dam average daily water temperature Draft 2013 Annual Report 126 May 2014

142 Figure 5.1e Rock Island Dam average daily water temperature Table 5.5. Number of days 2013 water temperature > 68 o F Dam Number of days > 68 Degrees Fahrenheit Bonneville 71 Mid-July through mid-september (69 days forebay and 71 days tailwater) McNary 65 Mid-July through mid-september (64 days forebay and 65 days tailwater) Priest Rapids 40 August through mid-september (40 days forebay and 37 days tailwater) Rock Island 16 September (both forebay and tailwater) Lower Granite 13 Late August and some days in September (13 days forebay and 6 days tailwater) In the lower Columbia River at Bonneville Dam daily average water temperatures were greater than 68ºF for 71 days from mid-july through mid-september. In the mid-columbia River at McNary Dam water temperatures were greater than 68ºF for 65 days from mid-july through mid-september. In the Upper Columbia River, there were 40 days when the water temperature was greater than 68ºF at Priest Rapids Dam from August through mid-september. At Rock Island Dam, water temperatures were greater than 68ºF for 16 days in both the forebay and Draft 2013 Annual Report 127 May 2014

143 tailwater in September. At Lower Granite Dam, water temperatures were greater than 68ºF for 13 days in late August and some days in September. 2. Adult Facilities Inspection Program The federal and state fish and wildlife agencies fund the annual Fish Facilities Inspection Program. An annual report is prepared each year, summarizing the inspections and whether or not passage facilities were operated within acceptable operations criteria. The Annual Fish Facilities Inspection Report is available at Fishway inspections by the State and Federal fishery agencies were completed at the 13 mainstem dams between March and October of 2013 with NOAA inspecting Bonneville, McNary, Priest Rapids, and Wanapum dams; WDFW inspecting Rock Island, Rocky Reach, and Wells dams; and ODFW inspecting The Dalles, John Day, Ice Harbor, Lower Monumental, Little Goose, and Lower Granite dams. Factors affecting fishway operations and/or the ability to inspect fishways at the mainstem dams during the 2013 fish passage season are listed below: Bonneville Dam: Head differential readings were below criteria at the Bradford south entrance during three of nine inspections in 2013 along with a low gate depth reported during the March inspection. Gate depths were below criteria at the A-branch entrance during both the March and June inspections and head differential was low during the May inspection. The B-branch entrance was out of head differential criteria during the September inspection and no reading could be obtained due to unreadable staff gauges and the PLC being out of service during the July inspection. Not clean staff gauges were reported during three of nine inspections at B-branch in At the Cascade Island entrance, staff gauges were reported as not clean during six of nine inspections and no readings for head differential could be obtained during the July inspection due to non-clean staff gauges and out of service PLC. Fish Turbine Unit Two (F2) was out of service during the October and November inspections. During the May inspection several Washington Shore north floating orifice gates were stuck and overtopping. The Washington Shore Fishway exit was reported as not clean during the October inspection. John Day Dam: Fish Pump #2 was out of service during the July fishway inspection (the south shore fishway was still able to achieve all fishway criteria during this inspection). All north fishway pumps were offline during the March inspection resulting in the fishway being at orifice flow and no readings were obtained. McNary Dam: Fish Pump #2 was out of service during the entire 2013 inspection season (the project did meet gate depth and head differential criteria during all of 2013 with two pumps). The southern collection channel velocity was below the 1.5 fps criteria during all inspections in The Washington Shore exit was reported as not clean during the April fishway inspection. Draft 2013 Annual Report 128 May 2014

144 Ice Harbor Dam: Multiple gate depths did not meet criteria; however in all cases, gates were operated as low as possible (on sill). During the May inspection the head differential at NFE-2 was below criteria (0.8 feet). Multiple staff gauges during the last inspection of the year (October) were reported as not legible. Lower Monumental Dam: Multiple entrance gate depths were below criteria (in all cases entrances were operated as low as possible on sill). There was debris build-up at the North Shore picketed leads during both the August and October inspections. Little Goose Dam: Multiple entrance gate depths were below criteria (in all cases entrances were operated as low as possible on sill and weirs at fixed elevation at the North Shore fishway). Fish Pump #3 was out of service during the first four inspections of During the September inspection, it was noted that one panel of the fall-out fence appeared to be missing. Lower Granite Dam: Multiple entrance head differentials were below criteria. Established shrubbery on the exit debris containment structure made it difficult to inspect the exit (the exit was reported as clean during all inspections). Over the summer of 2013, adult passage at Lower Granite Dam was impeded by excessive water temperatures in the ladder creating a large temperature differential between the ladder and the tailrace water; adults passing through the ladder did respond to the initiation of two emergency pumps that drew in cooler water to the fishway. Priest Rapids Dam: The water velocity in the collection channel was slightly below criteria during the August inspection. The head differential at RSE-1 was slightly below criteria during the May inspection. Rock Island Dam: During the August inspection, all right bank entrances recorded head differentials slightly below criteria. Wells Dam: Several staff gauges were reported as not clean or readable during the October inspection. F. Adult Fish Counts/Conclusions 1. Spring Chinook When considering the passage duration of each race of Chinook, it is important to remember that the dates determining passage of spring, summer and fall Chinook are set by convention. In reality, there is variability and overlap in the passage of each race of Chinook during the time periods between the peak passage periods of each race of Chinook. The 2013 adult spring Chinook counts decreased throughout most of the basin when compared to both the 2012 and 10-year average counts, with the exception of the counts at Rocky Reach Dam and Wells Dam in the upper Columbia. At the Columbia and Snake River dams, the 2013 counts were 57% of the 2012 counts on average and 71% of the 10-year average counts on average. The Willamette River counts also decreased. The 2013 Willamette Falls Dam adult spring Chinook counts were about 78% of the 2012 counts and 60% of the 10-year average counts. In the upper Columbia, the 2013 Draft 2013 Annual Report 129 May 2014

145 counts slightly increased. The 2013 adult spring Chinook counts were about 119% of the 2012 counts on average and about 142% of the 10-year average counts on average. The 2013 spring Chinook jack counts significantly increased throughout the basin when compared to both the 2012 counts and the 10-year average counts. At the Columbia and Snake River dams, the 2013 counts were 445% of the 2012 counts on average and 192% of the 10-year average counts on average. The largest increase in 2013 spring Chinook jack counts was at Lower Monumental Dam where the counts were 659% of the 2012 counts and 258% of the 10-year average counts. The 2013 Willamette Falls spring Chinook jack counts were about 127% of the 2012 counts and 146% of the 10- year average counts. The length of the 90% passage duration at Bonneville Dam (hereafter referred to as duration) of the 2013 adult spring Chinook run was only one day longer than the 2012 duration, while being 12 days shorter than the 10-year average (Table 5.7a). 2. Summer Chinook The 2013 adult summer Chinook counts slightly increased throughout the Columbia River compared to both the 2012 and 10-year average counts. In the Columbia River, the 2013 adult summer Chinook counts were 128% of the 2012 counts on average and 130% of the 10-year average counts. In the Snake River, the 2013 adult summer Chinook counts decreased when compared to the 2012 and 10-year average counts. In the Snake River, the 2013 adult summer Chinook were 74% of the 2012 average and 60% of the 10-year average counts. The 2013 summer Chinook jack counts increased throughout most of the basin when compared to both the 2012 counts and the 10-year average counts. At the Columbia River dams, the 2013 counts were 202% of the 2012 counts on average and 129% of the 10-year average counts. At the Snake River dams, the 2013 counts were 455% of the 2012 counts on average and 156% of the 10-year average counts. When considering the passage duration of each race of Chinook, it is important to remember that the dates established by the region determining passage of spring, summer and fall Chinook are set by convention. In reality, there is variability and overlap in passage of each race of Chinook during the time periods between peak passage periods of each race of Chinook. The 90% duration of the 2013 adult summer Chinook run was one day longer than the 2012 run and 3 days longer than the 10-year average run. 3. Fall Chinook The 2013 adult fall Chinook counts significantly increased throughout most of the basin when compared to both the 2012 counts and the 10-year average counts, while the counts decreased in the Willamette River when compared with 2012 counts. In the lower and mid-columbia, the 2013 adult fall Chinook counts were 265% of the 2012 counts on average and 277% of the 10-year average counts. In the upper Columbia, the counts were 158% of the 2012 counts on average and 260% of the 10-year average counts. The 2013 adult fall Chinook counts increased the most at the Snake River Dams. The 2013 counts in the Snake River were 492% of the 2012 counts on average Draft 2013 Annual Report 130 May 2014

146 and 577% of the 10-year average counts. In the Willamette River, the 2013 adult fall Chinook counts were 89% of the 2012 counts on average, while being 126% of the 10- year average counts. The 2013 fall Chinook jack counts decreased in the lower and mid-columbia and Willamette Rivers, while increasing in the Snake River and Upper Columbia when compared to the 2012 counts. The 2013 fall Chinook jack counts increased throughout the basin when compared to the 10-year average count. In the lower and mid- Columbia, the 2013 fall Chinook jack counts were 92% of the 2012 counts on average, while being 181% of the 10-year average counts. In the Willamette River, the 2013 fall Chinook jacks were 95% of the 2012 count, while being 155% of the 10-year average counts. In the upper Columbia, the counts were 102% of the 2012 counts on average and 162% of the 10-year average counts. The 2013 counts in the Snake River were 168% of the 2012 counts and 292% of the 10-year average counts. When considering the passage duration of each race of Chinook, it is important to remember that the dates established by the region determining passage of spring, summer and fall Chinook are set by convention. In reality, there is variability and overlap in passage of each race of Chinook during the time periods between peak passage periods of each race of Chinook. The duration of the 2013 adult fall Chinook run was 5 days longer than the 2012 run and 3 days longer than the 10-year average run. (Table 5.7c). Tule Fall Chinook o The estimated number of adult tule fall Chinook at Bonneville Dam in 2013 was 62,693 with 14,978 tules arriving at Spring Creek NFH (Figure 5.13), located in the Bonneville Dam pool (Ahrens, 2014). The 2013 tule estimated numbers increased at Bonneville Dam, while decreasing at Spring Creek NFH when compared to the 2012 estimated counts. The total 2013 adult tule fall Chinook at Bonneville were about 124% of the 2012 estimated count of 50,320. The 2013 Spring Creek NFH count was about 60% of the 2012 count of 24,860 and 48% of the 10-year average count of 31,335. The overall general decreases are the result of planned modifications of the Bonneville pool tule fall Chinook program at Spring Creek Hatchery. The decreases in Tule Fall Chinook in Bonneville Pool are the result of changes in the Spring Creek Hatchery production and release program. As part of this program some Tule fall Chinook are transferred from Spring Creek Hatchery to Bonneville Hatchery for release below Bonneville Dam. The goal of this program is to reduce the number of Tule Fall Chinook returning to the Bonneville pool and increase the number of upriver bright fall Chinook returning to Bonneville pool. o The tule jack fall Chinook counts increased at Spring Creek NFH in 2013 when compared to The 2013 tule jack count at Spring Creek NFH of 3,671 was about 161% of the 2012 count of 2,275. Draft 2013 Annual Report 131 May 2014

147 Upper Bright Fall Chinook o The bright component of the fall Chinook run is bound for Little White Salmon, Klickitat, Deschutes, John Day, and Umatilla rivers in the lower Columbia River reach, as well as mainstem and tributaries of the Mid-Columbia and Snake River reaches. The 2013 count of adult fall Chinook (bright component) that arrived at McNary Dam (Figure 5.14) of 454,991 represent an increase when compared to the 2012 count of 174,461. The 2013 count was about 261% of the 2012 count and 329% of the 10-year average of 138, Coho Increases in coho production programs in the Upper Columbia and Middle Columbia in recent years affect the comparison of recent coho dam counts with historical years. The 2013 adult coho dam counts decreased significantly through most of the basin except in the lower Columbia and Willamette Rivers. The 2013 adult coho counts were 58% of the 2012 counts on average and 52% of the 10-year average counts at the mid- Columbia and Snake River dams. At Willamette Falls, the 2013 adult coho counts were 284% of the 2012 counts and 233% of the 10-year average counts. At Bonneville Dam in the lower Columbia River, the 2013 adult coho counts were 108% of the 2012 counts, while being only about 50% of the 10-year average counts. The 2013 coho jack counts varied (some counts increased and others decreased) throughout the region when compared to the 2012 counts and the 10-year average counts. At Bonneville Dam, the 2013 coho jack counts were 141% of the 2012 counts and 107% of the 10-year average counts. The McNary Dam 2013 coho jack counts were 122% of the 2012 counts, while being 91% of the 10-year average counts. The Priest Rapids Dam 2013 coho jack counts were 30% of the 2012 counts and 75% of the 10-year average counts. The Lower Granite Dam 2013 coho jack counts were 177% of the 2012 counts and 117% of the 10-year average counts. The Willamette Falls 2013 coho jack counts were 64% of the 2012 counts and 214% of the 10-year average counts. The duration of the 2013 adult coho run was 9 days longer than 2012 run and 10 days longer than 10-year average run. 5. Sockeye The 2013 adult sockeye counts decreased significantly in the Columbia River when compared to the 2012 counts, while the counts increased slightly when compared to the 10-year average counts. The 2013 sockeye counts increased in the Snake River when compared to both the 2012 and 10-year average counts. In the Columbia, the 2013 adult sockeye counts were 38% of the 2012 counts on average and 105% of the 10-year average counts. In the Snake River, the 2013 adult sockeye counts were 197% of the 2012 counts on average and 180% of the 10-year average counts on average. The length duration of the 2013 adult sockeye run was 9 days longer than the 2012 run and 8 days longer than the 10-year average run. As has occurred in past years sockeye adult count disparities occurred between McNary Dam and Priest Rapids Dam. The total count of sockeye at McNary was 134,202, at Ice Draft 2013 Annual Report 132 May 2014

148 Harbor Dam on the Snake the adult sockeye count was 895 and 163,079 at Priest Rapids Dam. This count disparity indicates that sockeye may migrate through navigation locks when possible. 6. Steelhead Generally throughout the region, the 2013 adult steelhead counts decreased when compared to the 2012 counts and the 10-year average counts. The 2013 adult steelhead counts were 88% of the 2012 counts on average and 63% of the 10-year average counts on average. The duration of the 2012 adult steelhead run was 19 days shorter than the 2012 run and 9 days shorter than the 10-year average run. Steelhead count data is reported as total steelhead and wild steelhead. The wild steelhead count is included in the total count. However, the wild steelhead count is actually a count of steelhead without fin clips (i.e., unclipped). Not all hatchery steelhead are fin clipped, therefore an unclipped steelhead is not necessarily wild. The 2013 wild (unclipped) steelhead counts slightly increased in the lower and mid- Columbia and Snake Rivers, while slightly decreasing in the upper Columbia when compared with the 2012 counts. The 2013 wild steelhead counts decreased throughout the region when compared with the 10-year average counts. At the lower and mid- Columbia and Snake River dams, the 2013 wild (unclipped) steelhead counts were 111% of the 2012 counts on average. At the upper Columbia dams, the unclipped steelhead counts were 86% of the 2012 counts on average. At Columbia and Snake River dams, the 2013 adult wild steelhead counts were 77% of the 10-year average counts on average. The 2013 count of A-run summer steelhead was 166,532 at Bonneville Dam, which was about 108% of the 2012 count of 154,605, while being 71% of the 10-year average count of 235,385. The 2013 count of 63,064 B-run summer steelhead at Bonneville Dam was about 86% of the 2012 count of 73,195 and about 52% of the 10-year average count of 120, Lamprey Lamprey historically numbered in the hundreds of thousands at Bonneville Dam. The highest recorded count at Bonneville Dam was 379,509 in 1969 (Figure 5.12). There are no lamprey counts available at Bonneville Dam from 1970 through 1995, as shown in Figure There has been a dramatic decline in the distribution and abundance of lampreys. This is because of several factors including the construction of dams and diversions, degradation of spawning habitat, and the degradation of rearing habitat. Turbine screen systems at mainstem dams impinge juvenile lamprey migrating downstream to the ocean (Brostrom et al., 2010). The 2013 Bonneville Dam adult lamprey count of 23,970 was 82% of the 2012 count of 29,224 and 69% of the 10-year average count of 34,562. Draft 2013 Annual Report 133 May 2014

149 8. Pink and Chum In 2013, only 508 pink salmon crossed Bonneville Dam, while in 2012, one pink salmon crossed Bonneville Dam. In 2013, 167 adult chum crossed Bonneville Dam which was 102 more fish than the 2012 count of 65. Documentation is lacking for specific tributary spawning above Bonneville Dam. It is interesting to note that in 2011 pink salmon were seen all the way up to Rocky Reach Dam, as well as in the Snake River (McCann, 2012). In 2011, the adult pink salmon dam count at Rock Island Dam was 26 and at Rocky Reach Dam the count was 3 adults (Mosley, 2012). Documentation for specific tributary spawning of pink salmon above Bonneville Dam is lacking. However pink salmon fry have been noted in the Smolt Monitoring Program at Bonneville Dam. Draft 2013 Annual Report 134 May 2014

150 Table 5.6a Spring Chinook Cumulative 2013 Adult Passage at Mainstem Dams Spring Chinook Percentage of Percentage of Yr Avg Yr Avg Yr Avg Dam Adult Jack Adult Jack Adult Jack Adult Jack BON 83,345 33, ,089 7, ,713 20, % 58.8% 445.5% 166.4% TDA 69,202 32, ,087 7, ,368 16, % 64.5% 450.3% 191.1% JDA 56,991 28, ,655 6,755 92,410 15, % 61.7% 428.7% 182.4% MCN 52,176 22, ,763 4,787 83,990 13, % 62.1% 465.4% 160.8% IHR 38,017 18,611 71,957 2,905 58,986 8, % 64.5% 640.7% 217.5% LMN 36,470 19,053 68,608 2,891 58,025 7, % 62.9% 659.0% 258.2% LGS 35,072 19,443 68,247 3,449 53,406 8, % 65.7% 563.7% 230.7% LGR 35,031 19,940 66,366 3,525 53,382 9, % 65.6% 565.7% 202.4% PRD 13,725 1,298 19,495 1,015 15,225 1, % 90.1% 127.9% 92.3% WAN 13,715 1,661 19, ,699 2, % NA 170.7% NA RIS 13,345 3,100 19, ,248 2, % 93.7% 387.5% 138.6% RRH 6,841 2,101 6, , % 128.9% 457.7% 246.3% WEL 7,133 2,980 5, , % 154.5% 425.7% 338.6% WFA 27,897 1,664 35,899 1,314 46,153 1, % 60.4% 126.6% 145.8% Table 5.6b Summer Chinook Cumulative 2013 Adult Passage at Mainstem Dams Summer Chinook Percentage of Percentage of Yr Avg Yr Avg Yr Avg Dam Adult Jack Adult Jack Adult Jack Adult Jack BON 93,097 26,186 81,663 12,235 87,543 17, % 106.3% 214.0% 148.9% TDA 85,639 20,750 69,222 10,392 74,538 13, % 114.9% 199.7% 149.2% JDA 75,248 19,714 60,814 10,415 67,514 14, % 111.5% 189.3% 135.0% MCN 75,741 14,808 64,428 5,104 63,310 10, % 119.6% 290.1% 136.5% IHR 11,912 6,321 14,182 1,481 17,476 4, % 68.2% 426.8% 148.7% LMN 11,765 7,703 15,150 1,611 18,803 4, % 62.6% 478.2% 182.8% LGS 10,120 7,632 14,748 1,613 17,544 4, % 57.7% 473.2% 155.6% LGR 8,423 7,572 13,163 1,717 16,010 5, % 52.6% 441.0% 136.2% PRD 71,083 3,174 50,667 1,994 53,926 2, % 131.8% 159.2% 121.5% WAN 69,983 2,189 50,588 1,515 47,124 1, % NA 144.5% NA RIS 68,386 3,986 52,184 3,343 51,396 5, % 133.1% 119.2% 73.0% RRH 59,685 4,044 45,528 2,775 39,283 4, % 151.9% 145.7% 93.8% WEL 49,451 4,264 38,588 3,271 28,793 2, % 171.7% 130.4% 152.2% WFA NA NA NA NA NA NA NA NA NA NA Draft 2013 Annual Report 135 May 2014

151 Table 5.6c Fall Chinook Cumulative 2013 Adult Passage at Mainstem Dams Fall Chinook Percentage of Percentage of Dam Yr Avg Yr Avg Yr Avg Adult Jack Adult Jack Adult Jack Adult Jack BON 953, , , , ,955 61, % 245.1% 89.4% 181.5% TDA 602,562 87, , , ,901 51, % 272.8% 80.7% 171.0% JDA 439,480 89, ,974 91, ,331 45, % 262.6% 98.1% 198.7% MCN 454,991 54, ,461 53, ,154 31, % 329.3% 101.3% 172.4% IHR 58,143 19,170 38,546 21,554 24,323 14, % 239.0% 88.9% 131.2% LMN 53,399 23,031 33,518 22,883 22,159 14, % 241.0% 100.6% 162.5% LGS 55,190 21,985 34,843 19,219 21,343 11, % 258.6% 114.4% 193.7% LGR 56,565 22,395 34,688 21,990 18,920 14, % 299.0% 101.8% 158.4% PRD 263,924 18,522 54,825 10,491 36,929 5, % 714.7% 176.6% 328.1% WAN 92,559 7,546 21,599 5,228 20,697 4, % NA 144.3% NA RIS 57,384 12,052 11,102 5,540 11,337 3, % 506.2% 217.5% 384.7% RRH 48,410 8,109 8,838 4,236 7,633 2, % 634.2% 191.4% 354.0% WEL 17,354 1,580 3,559 1,417 3,822 1, % 454.1% 111.5% 102.6% WFA 1, , , % 125.8% 95.3% 154.9% Table 5.6d Coho Cumulative 2013 Adult Passage at Mainstem Dams Coho Percentage of Percentage of Dam Yr Avg Yr Avg Yr Avg Adult Jack Adult Jack Adult Jack Adult Jack BON 59,610 7,148 54,968 5, ,343 6, % 49.5% 141.4% 106.8% TDA 24,110 2,572 31,144 2,875 42,203 3, % 57.1% 89.5% 74.9% JDA 16,718 1,421 30,216 3,643 39,405 4, % 42.4% 39.0% 35.1% MCN 12,128 1,753 17,368 1,433 21,777 1, % 55.7% 122.3% 90.7% IHR 2, , , % 79.0% 120.5% 194.2% LMN 2, , , % 74.3% 112.3% 128.0% LGS 1, , , % 69.2% 157.3% 181.8% LGR 2, , , % 76.5% 177.2% 116.6% PRD 3, ,381 1,577 7, % 47.5% 30.3% 75.4% WAN 1, , , % NA 25.6% NA RIS 2, , , % 21.2% 155.6% 40.1% RRH , , % 16.3% 111.6% 30.0% WEL , , % 34.1% 128.6% NA WFA 18,629 4,111 6,571 6,370 8,006 1, % 232.7% 64.5% 214.1% Draft 2013 Annual Report 136 May 2014

152 Table 5.6e Sockeye Cumulative 2013 Adult Passage at Mainstem Dams Sockeye Percentage of Yr Avg Yr Avg Dam Adult Adult Adult Adult BON 185, , , % 104.5% TDA 161, , , % 110.7% JDA 155, , , % 104.3% MCN 134, , , % 106.7% IHR % 210.6% LMN 1, % 191.3% LGS % 196.1% LGR % 123.5% PRD 163, , , % 105.4% WAN 155, , , % NA RIS 159, , , % 104.5% RRH 131, , , % 101.4% WEL 129, , , % 105.2% WFA NA NA NA NA NA Table 5.6f Steelhead Cumulative 2013 Adult Passage at Mainstem Dams Steelhead Percentage of Percentage of Yr Avg Yr Avg Yr Avg Dam Adult Wild Adult Wild Adult Wild Adult Wild BON 234,047 99, ,303 85, , , % 64.3% 116.0% 89.0% TDA 190,750 80, ,640 71, ,611 87, % 65.4% 112.8% 91.6% JDA 155,742 66, ,083 61, ,213 85, % 54.4% 107.2% 77.1% MCN 144,354 55, ,018 53, ,286 69, % 58.6% 104.9% 80.3% IHR 116,162 32, ,269 27, ,739 43, % 63.6% 119.0% 74.5% LMN 106,649 33, ,523 28, ,042 47, % 56.4% 118.7% 70.7% LGS 95,871 29,587 98,278 28, ,894 41, % 54.2% 104.7% 70.9% LGR 107,910 33, ,675 31, ,578 44, % 60.1% 107.0% 76.4% PRD 15,011 NA 17,230 NA 19,637 NA 87.1% 76.4% NA NA WAN 12,325 NA 15,516 NA 20,265 NA 79.4% 60.8% NA NA RIS 11,501 6,062 15,457 6,510 18,193 8, % 63.2% 93.1% 71.6% RRH 9,204 4,585 13,106 5,400 14,494 6, % 63.5% 84.9% 74.0% WEL 7,222 3,421 9,778 4,248 10,983 4, % 65.8% 80.5% 73.5% WFA 18,237 NA 32,193 NA 26,677 NA 56.6% 68.4% NA NA Note: This report uses historical counting schedule date ranges. Some steelhead divert into non-natal streams during the summer, but go back to the mainstem and swim upstream to natal streams late in the year and early winter when dam counts are not done. These fish will not be counted at upstream dams. Draft 2013 Annual Report 137 May 2014

153 Table 5.7a 2013 Adult Spring Chinook Run Duration at Bonneville Dam* Spring Chinook - Length of Run Year 1% 5% 10% 90% 95% 99% 80% of run (between 10% and 90%) 90% of run (between 5% and 95%) Apr 22-Apr 24-Apr 21-May 26-May 30-May Apr 23-Apr 24-Apr 20-May 26-May 30-May Apr 26-Apr 28-Apr 16-May 21-May 30-May Apr 13-Apr 16-Apr 16-May 25-May 30-May Apr 22-Apr 25-Apr 25-May 28-May 1-Jun Apr 14-Apr 20-Apr 20-May 26-May 30-May Apr 16-Apr 19-Apr 22-May 27-May 31-May Apr 29-Apr 1-May 20-May 24-May 28-May Apr 21-Apr 23-Apr 26-May 29-May 31-May Apr 13-Apr 15-Apr 19-May 25-May 30-May Mar 26-Mar 31-Mar 20-May 26-May 31-May Mar 10-Apr 15-Apr 18-May 26-May 31-May Year Avg 20-Mar 11-Apr 17-Apr 21-May 27-May 31-May *Note: Spring, summer, and fall Chinook race dam counts are determined by run schedules established by personnel at dam operating agencies. Duration refers to the length of 90% passage duration at Bonneville Dam. Table 5.7b 2013 Adult Summer Chinook Run Duration at Bonneville Dam* Summer Chinook - Length of Run Year 1% 5% 10% 90% 95% 99% 80% of run (between 10% and 90%) 90% of run (between 5% and 95%) Jun 3-Jun 6-Jun 16-Jul 24-Jul 29-Jul Jun 2-Jun 4-Jun 16-Jul 22-Jul 28-Jul Jun 3-Jun 5-Jun 16-Jul 23-Jul 29-Jul Jun 2-Jun 3-Jun 11-Jul 19-Jul 28-Jul Jun 3-Jun 5-Jun 14-Jul 19-Jul 28-Jul Jun 4-Jun 6-Jun 14-Jul 20-Jul 28-Jul Jun 4-Jun 6-Jun 19-Jul 24-Jul 30-Jul Jun 5-Jun 8-Jun 14-Jul 21-Jul 28-Jul Jun 3-Jun 7-Jun 17-Jul 22-Jul 28-Jul Jun 3-Jun 6-Jun 15-Jul 20-Jul 29-Jul Jun 4-Jun 7-Jun 18-Jul 23-Jul 30-Jul Jun 4-Jun 6-Jun 17-Jul 24-Jul 30-Jul Year Avg 1-Jun 3-Jun 5-Jun 16-Jul 21-Jul 30-Jul *Note: Spring, summer, and fall Chinook race dam counts are determined by run schedules established by personnel at dam operating agencies. Duration refers to the length of 90% passage duration at Bonneville Dam. Draft 2013 Annual Report 138 May 2014

154 Table 5.7c 2013 Adult Fall Chinook Run Duration at Bonneville Dam* Fall Chinook - Length of Run Year 1% 5% 10% 90% 95% 99% 80% of run (between 10% and 90%) 90% of run (between 5% and 95%) Aug 22-Aug 27-Aug 26-Sep 5-Oct 17-Oct Aug 22-Aug 27-Aug 24-Sep 30-Sep 13-Oct Aug 20-Aug 28-Aug 27-Sep 5-Oct 17-Oct Aug 23-Aug 27-Aug 26-Sep 1-Oct 12-Oct Aug 17-Aug 21-Aug 21-Sep 29-Sep 14-Oct Aug 22-Aug 24-Aug 21-Sep 28-Sep 13-Oct Aug 17-Aug 23-Aug 1-Oct 10-Oct 23-Oct Aug 23-Aug 27-Aug 30-Sep 8-Oct 31-Oct Aug 25-Aug 30-Aug 25-Sep 1-Oct 16-Oct Aug 27-Aug 29-Aug 25-Sep 1-Oct 16-Oct Aug 27-Aug 30-Aug 22-Sep 28-Sep 16-Oct Aug 23-Aug 25-Aug 20-Sep 26-Sep 13-Oct Year Avg 5-Aug 22-Aug 27-Aug 25-Sep 2-Oct 17-Oct *Note: Spring, summer, and fall Chinook race dam counts are determined by run schedules established by personnel at dam operating agencies. Duration refers to the length of 90% passage duration at Bonneville Dam. Table 5.7d 2013 Adult Coho Run Duration at Bonneville Dam* Coho - Length of Run Year 1% 5% 10% 90% 95% 99% 80% of run (between 10% and 90%) 90% of run (between 5% and 95%) Aug 28-Aug 2-Sep 21-Oct 1-Nov 9-Nov Aug 29-Aug 1-Sep 18-Oct 24-Oct 2-Nov Aug 26-Aug 1-Sep 9-Oct 13-Oct 20-Oct Aug 30-Aug 3-Sep 21-Oct 28-Oct 5-Nov Aug 24-Aug 27-Aug 19-Oct 24-Oct 31-Oct Aug 31-Aug 2-Sep 14-Oct 18-Oct 27-Oct Aug 30-Aug 1-Sep 22-Oct 27-Oct 9-Nov Aug 26-Aug 29-Aug 19-Oct 26-Oct 14-Nov Aug 1-Sep 3-Sep 12-Oct 17-Oct 27-Oct Aug 30-Aug 1-Sep 16-Oct 20-Oct 28-Oct Aug 30-Aug 1-Sep 15-Oct 19-Oct 26-Oct Aug 31-Aug 8-Sep 20-Oct 26-Oct 10-Nov Year Avg 19-Aug 28-Aug 1-Sep 17-Oct 22-Oct 1-Nov *Note: Spring, summer, and fall Chinook race dam counts are determined by run schedules established by personnel at dam operating agencies. Duration refers to the length of 90% passage duration at Bonneville Dam. Draft 2013 Annual Report 139 May 2014

155 Table 5.7e 2013 Adult Sockeye Run Duration at Bonneville Dam* Sockeye - Length of Run Year 1% 5% 10% 90% 95% 99% 80% of run (between 10% and 90%) 90% of run (between 5% and 95%) Jun 12-Jun 15-Jun 11-Jul 15-Jul 22-Jul Jun 15-Jun 18-Jun 7-Jul 9-Jul 13-Jul Jun 18-Jun 21-Jun 11-Jul 14-Jul 20-Jul Jun 15-Jun 18-Jun 5-Jul 9-Jul 14-Jul Jun 13-Jun 16-Jun 4-Jul 7-Jul 14-Jul Jun 13-Jun 15-Jun 1-Jul 4-Jul 11-Jul Jun 11-Jun 14-Jun 6-Jul 12-Jul 20-Jul Jun 12-Jun 15-Jun 6-Jul 10-Jul 21-Jul Jun 13-Jun 16-Jun 9-Jul 14-Jul 21-Jul Jun 10-Jun 13-Jun 5-Jul 9-Jul 16-Jul Jun 14-Jun 17-Jun 9-Jul 13-Jul 22-Jul Jun 16-Jun 19-Jun 8-Jul 12-Jul 18-Jul Year Avg 7-Jun 14-Jun 16-Jun 6-Jul 9-Jul 18-Jul *Note: Spring, summer, and fall Chinook race dam counts are determined by run schedules established by personnel at dam operating agencies. Duration refers to the length of 90% passage duration at Bonneville Dam. Table 5.7f 2013 Adult Steelhead Run Duration at Bonneville Dam* Steelhead - Length of Run Year 1% 5% 10% 90% 95% 99% 80% of run (between 10% and 90%) 90% of run (between 5% and 95%) Mar 8-Jul 18-Jul 15-Sep 26-Sep 11-Oct Mar 24-Jun 24-Jun 21-Sep 1-Oct 21-Oct Mar 6-Jul 6-Jul 14-Sep 22-Sep 9-Oct Mar 22-Jun 3-Jul 13-Sep 22-Sep 9-Oct May 10-Jul 21-Jul 12-Sep 22-Sep 12-Oct Apr 30-Jun 10-Jul 15-Sep 20-Sep 6-Oct Mar 5-Jul 17-Jul 18-Sep 27-Sep 16-Oct Feb 4-Jul 18-Jul 22-Sep 2-Oct 11-Nov May 3-Jul 13-Jul 27-Sep 5-Oct 20-Oct Mar 19-Jun 6-Jul 22-Sep 30-Sep 15-Oct Feb 28-Jun 11-Jul 17-Sep 26-Sep 26-Oct Mar 26-Jun 10-Jul 22-Sep 30-Sep 16-Oct Year Avg 20-Mar 30-Jun 12-Jul 18-Sep 27-Sep 17-Oct *Note: Spring, summer, and fall Chinook race dam counts are determined by run schedules established by personnel at dam operating agencies. Duration refers to the length of 90% passage duration at Bonneville Dam. Draft 2013 Annual Report 140 May 2014

156 Figure 5.2. Spring Chinook Adult Passage Draft 2013 Annual Report 141 May 2014

157 Figure 5.3. Spring Chinook Jack Passage Draft 2013 Annual Report 142 May 2014

158 Figure 5.4. Summer Chinook Adult Passage Draft 2013 Annual Report 143 May 2014

159 Figure 5.5. Summer Chinook Jack Passage Draft 2013 Annual Report 144 May 2014

160 Figure 5.6. Fall Chinook Adult Passage Draft 2013 Annual Report 145 May 2014

161 Figure 5.7 Fall Chinook Jack Passage Draft 2013 Annual Report 146 May 2014

162 Figure 5.8. Coho Adult Passage Draft 2013 Annual Report 147 May 2014

163 Figure 5.9. Coho Jack Passage Draft 2013 Annual Report 148 May 2014

164 Figure Sockeye Adult Passage Draft 2013 Annual Report 149 May 2014

165 Figure Steelhead Adult Passage Draft 2013 Annual Report 150 May 2014

166 Figure Historical Annual Bonneville Dam Adult Lamprey Count Figure Historical Spring Creek National Fish Hatchery tule fall Chinook counts Draft 2013 Annual Report 151 May 2014

167 Figure Historical upriver bright counts at McNary Dam G. Predicted Run Sizes Both historical and current Bonneville Dam counts assist TAC in developing run size forecasts for the following year. The preseason forecasts are an essential tool for salmon managers when making decisions about potential salmon seasons and the associated salmon harvest. In addition to the preseason forecasts, the TAC utilizes current and historical Bonneville Dam counts in-season to track the progress of various salmon and steelhead runs, and salmon managers use the information and adjust fisheries accordingly. Table 5.8 lists some of the 2013 TAC run size predictions and actual returns (TAC, 2014). The table also lists the 2014 TAC run size forecasts. For more information, see the following websites: and (Columbia River Compact Joint Staff Reports) Draft 2013 Annual Report 152 May 2014

168 Table 5.8. TAC 2013 run size forecast and actual returns 1 Columbia River Mouth Adult Fish Returns Actual and Forecasts** 2013 Forecast 2013 Return 2014 Forecast Spring Chinook Total Spring Chinook 225, , ,000 Willamette 59,800 47,300 58,700 Sandy 6,100 5,700 5,500 Cowlitz* 5,500 9,500 7,800 Kalama* 700 1, Lewis* 1,600 1,600 1,100 Select Areas 9,900 7,000 7,400 Lower River total 83,600 72,100 81,000 Wind* 3,000 3,600 8,500 Drano Lake* 4,900 7,300 13,100 Klickitat* 2,200 1,800 2,500 Yakima* 7,300 7,100 9,100 Upper Columbia Total 14,300 18,000 24,100 Upper Columbia Wild 1,600 3,600 3,700 Snake River Spring/Summer Total 58,200 67, ,000 Snake River Wild 18,900 21,900 42,200 Upriver Total 141, , ,000 Summer Chinook Upper Columbia Total 73,500 67,600 67,500 Fall LRH - Lower River Hatch. 86, , ,700 Chinook LRW - Lower River Wild 14,300 25,800 33,400 BPH - Bonneville Pool Hatch. 36,300 86, ,200 URB - Upriver Bright 434, , ,000 Snake River Wild Wild 31,600 32,900 61,000 MCB Mid Col Bright 97, , ,200 BUB Bonn. Upr. Br. Hatch. 27,900 33,900 45,000 LRB L. River Brights Wild 1,300 1,700 1,900 PUB Pool Upr. Br. Hatch. 68, , ,300 SAB Select Area Br. Hatch. 8,900 23,400 10,100 Total Fall Chinook 678,600 1,268,400 1,510,600 Coho Early stock 288, , ,100 Late stock 145,100 84, ,200 Total Coho 433, , ,300 Sockeye Wenatchee 44,600 36,000 63,400 Okanogan 134, , ,500 Snake River Wild 1,250 1,100 1,200 Total Sockeye 180, , ,100 Steelhead Winter Wild winter steelhead Wild 15,700 15,600 16,100 Upriver Summer Upriver Skamania Index Total 16,600 5,800 8,600 (to Bonneville Dam) Wild 5,300 1,700 2,300 Group A-run Index Total 291, , ,400 Wild 83,500 90,500 82,400 Group B-run Index Total 31,600 11,500 31,000 Wild 7,900 2,900 6,500 Total Upr. Steelhead Total 339, , ,000 Wild 96,700 95,100 91, Table developed by the Technical Advisory Committee of US v Oregon states and tribal fishery co-managers. * Return to tributary mouth. ** Forecast predictions and actual returns developed by US v Oregon Technical Advisory Committee. Draft 2013 Annual Report 153 May 2014

169 I. Adult Section References Ahrens, Mark Personal telephone communication. Spring Creek National Fish Hatchery, Underwood, Washington. Boggs, C. T., Keefer, M. L., Peery, C. A., Bjornn, T. C. and Stuehrenberg, L. C a. Fallback, reascension, and adjusted fishway escapement estimates for adult Chinook salmon and steelhead at Columbia and Snake River dams. Transactions of the American Fisheries Society. 133: Boggs, C. T., Keefer, M. L. and Peery, C. A b. Adult Chinook salmon and steelhead fallback at Bonneville Dam, Idaho Cooperative Fish and Wildlife Research Unit, Technical Report for the U.S. Army Corps of Engineers, Portland, Oregon. Available: (March 2005). Brostrom, Jody, Luzier, Christina, Thompson, Katherine Best Management Practices to Minimize Adverse Effects to Pacific Lamprey (Entosphenus tridentatus). US Fish and Wildlife Service, Portland, Oregon. Available at: ctices%20for%20pacific%20lamprey%20april%202010%20version.pdf Busby, P.J., Wainwright, T.C, Bryant, G.J., Lierheimer, L.J., Waples, R.S., Waknitz, F.W. and Lagomarsino, I.V Status Reivew of West Coast Steelhead from Washington, Idaho, Oregon and California. Northwest Fisheries Science Center, NOAA, Seattle, WA. Available online at: Clabough, T.S., Jepson, M.A., Caudill, C.C., Peery, C.A Influence of Water Temperature on Adult Salmon and Steelhead Passage and Behavior at Lower Granite Dam, Department of Fish and Wildlife Resources, University of Idaho, Moscow, Idaho. Available at: Dauble, D.D. and Watson, D.G Spawning and Abundance of Fall Chinook Salmon in the Hanford Reach of the Columbia River, Pacific Northwest Laboratory, Battelle Memorial Institute, United States Department of Commerce, Oakridge, TN. Dauble, Dennis D., Robert P. Mueller, U.S. Department of Energy, Bonneville Power Administration, Division of Fish and Wildlife, Project No , Contract No. DE- AM BP99654, Master Agreement DE-AI79-BP62611, 81 electronic pages (BPA Report DOE/BP ). Fish Passage Center (FPC) Adult Fishway Inspections on the Columbia and Snake Rivers: 2013 Annual Report. Fish Passage Center, Portland OR. Available online at: Draft 2013 Annual Report 154 May 2014

170 Goniea, T.M., Keefer, M.L., Bjornn, T.C., Bennett, D.H. and Stuehrenburg, L.C Behavioral thermoregulation and slowed migration by adult fall Chinook salmon in response to high Columbia River water temperatures. Transactions of the American Fisheries Society. 135(2): Hicks, M Preliminary Review Draft Discussion Paper Evaluating Standards for Protecting Aquatic Life In Washington s Surface Water Quality Standards Temperature Criteria. Washington State Department of Ecology, Water Quality Program, Watershed Management Section. Olympia, Washington. Available online at: Independent Scientific Advisory Board Report of the Independent Scientific Advisory Board Review of the U.S. Army Corps of Engineers Capital Construction Program Part III. A. Adult Passage. ISAB, Northwest Power Planning Council, Portland, OR. Available at Joint Columbia Management Staff (JCMS) Joint staff report concerning the 2006 in-river commercial harvest of Columbia River fall Chinook salmon, summer steelhead, Coho salmon, chum salmon, and sturgeon, July 18, ODFW and WDFW, Vancouver, WA. Keefer, M. L., Caudill, C. C., Peery, C. A., and Bjornn, T.C Route selection in a large river during the homing migration of Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences. 63(8): Available at: Keefer, M. L., Peery, C. A., Bjornn, T. C., Jepson, M. A. and Stuehrenberg, L.C Hydrosystem, dam, and reservoir passage rates of adult Chinook salmon and steelhead in the Columbia and Snake rivers. Transactions of the American Fisheries Society 133: Keefer, M. L., Peery, C. A., Daigle, W. R., Jepson, M. A., Lee, S. R., Boggs, C. T., Tolotti, K. R. and Burke, B. J Escapement, harvest, and unknown loss of radio-tagged adult salmonids in the ColumbiaSnake River hydrosystem. Canadian Journal of Fisheries and Aquatic Sciences 62: LeFleur, Cindy Adult Fish Runs / Fisheries Review, presentation at the Columbia River Regional Forum, Technical Management Team, Year End Review, December 13, WDFW, Vancouver WA. Available at LeFleur, Cindy Personal communication. WDFW, Vancouver WA. LeFleur, Cindy Personal communication. WDFW, Vancouver WA. Draft 2013 Annual Report 155 May 2014

171 Lower Columbia Fish Recovery Board (LCFRB) Lower Columbia Salmon Recovery and Fish and Wildlife Plan. NPCC, Portland, Oregon. Available at: Ch%202%20Species.pdf McCann, Jerry Personal communication. FPC, Portland, OR. McCullough, D A Review and Synthesis of Effects of Alterations to the Water Temperature Regime on Freshwater Life Stages of Salmonids, with Special Reference to Chinook Salmon. Columbia Intertribal Fisheries Commission, Portland, OR. Prepared for the U.S. Environmental Protection Agency Region 10. Published as EPA 910-R Available online at: McCullough, D A Review and Synthesis of Effects of Alterations to the Water Temperature Regime on Freshwater Life Stages of Salmonids, with Special Reference to Chinook Salmon. Columbia Intertribal Fisheries Commission, Portland, OR. Prepared for the U.S. Environmental Protection Agency Region 10. Published as EPA 910-R Available online at: pdf Mosley, Thad Personal communication. Chelan PUD, Wenatchee, WA. Myers, J.M., R.G. Kope, G.J. Bryant, D. Teel, L.J. Lierheimer, T.C. Wainwright, W.S. Grand, F.W. Waknitz, K. Neely, S.T. Lindley, and R.S. Waples Status review of chinook salmon from Washington, Idaho, Oregon, and California. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-35, 443 p. National Marine Fisheries Service (NMFS) Endangered and threatened species; threatened status for Snake River spring/summer chinook salmon, threatened status for Snake River fall chinook salmon; Federal Register [Docket No , 22 April 1992] 57(78): , NMFS, Seattle, WA. National Marine Fisheries Service (NMFS) Factors for Decline: A Supplement to the Notice of Determination for West Coast Steelhead Under the Endangered Species Act. NMFS, Portland, Oregon. National Marine Fisheries Service Coastal Salmon Conservation: Working Guidance for Comprehensive Salmon Restoration Initiatives on the Pacific Coast. NMFS, Northwest Region, Seattle, WA. 6 p. National Oceanic and Atmospheric Administration (NOAA) Factors Contributing to the Decline of Chinook Salmon: An Addendum to the 1996 West Coast Steelhead Factors for Decline Report. NOAA, Portland, Oregon. Available at: Salmon-Listings/Salmon-Populations/Reports-and- Publications/loader.cfm?url=/commonspot/security/getfile.cfm&pageid=27109 Draft 2013 Annual Report 156 May 2014

172 NOAA Fisheries Report To Congress, Pacific Coastal Salmon Recovery Fund, Fiscal Years , Chapter 3 Status and Recovery of Listed Salmon Populations. PCSRF, Seattle WA. Available at Planning/PCSRF/upload/PCSRF-06-Ch3.pdf. Northwest and Southwest Fisheries Science Centers, West Coast Salmon Biological Review Team (WCSBRT), NOAA Updated Status of Federally Listed ESUs of West Coast Salmon and Steelhead. Northwest Fisheries Science Center, NOAA, Seattle, WA. Available online at: Northwest Fisheries Science Center The Tale of the Migrating Mini Jack. Northwest Fisheries Science Center, NOAA, Seattle, WA. Available online at: Naughton, George P., Caudill, C., Keefer, M., Bjornn, T., and Peery, C Fallback by Adult Sockeye Salmon at Columbia River Dams. North American Journal of Fisheries Management. 26: Northwest Power and Conservation Council (NPCC) Columbia River Basin Fish and Wildlife Program, Council document NPCC, Portland, Oregon. Available at: Paul R. Seaber, F. Paul Kapinos, and George L. Knapp Hydrologic Unit Maps, U.S. Geological Survey, Water Supply Paper USGS, Denver, Colorado. Available at: Reischel, T. S., and Bjornn, T. C Influence of fishway placement on fallback of adult salmon at the Bonneville Dam on the Columbia River. North American Journal of Fisheries Management 23: Scientific Review Team Independent Scientific Advisory Board (SRT) Review of Artificial Production of Anadromous and Resident Fish in the Columbia River Basin. Northwest Power Planning Council, Portland OR. Available at: TAC (Technical Advisory Committee) Columbia River Mouth Fish Returns 2013 Actual and 2014 Forecasts, May 7, WDFW, Olympia, Washington. Available at: ns_and_2014_forecasts.pdf United States Army Corps of Engineers (USACE), Walla Walla District Columbia River Salmon Migration Analysis System Configuration Study, Phase I, Main Report. USACE, Walla Walla, Washington. Available at: Draft 2013 Annual Report 157 May 2014

173 United States Army Corps of Engineers (USACE), Walla Walla District Annual Fish Passage Report, USACE, Walla Walla, Washington. Available at: United States Army Corps of Engineers (USACE), Northwestern Division, Water Quality Unit Dissolved Gas and Water Temperature Report. USACOE, Water Quality Unit Reservoir Control Center, Columbia Basin Water Management Division, Portland, Oregon. Available online at: U.S. Environmental Protection Agency EPA Region 10 Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards. EPA 910-B Region 10 Office of Water, Seattle, WA. United States Fish and Wildlife Service (USFWS), Oregon Department of Fish and Wildlife (ODFW), and Washington Department of Fish and Wildlife (WDFW) Ives Island study, spawning below Bonneville dam, March USFWS, WDFW, ODFW, Portland, OR. Available on at: Uusitalo, Nancy M Evaluate Factors Limiting Columbia River Gorge Chum Salmon Populations BPA Contract # FY 2002 Annual Report. U.S. Fish and Wildlife Service, Columbia River Fish Program Office, Habitat and Population Assessment Team, Portland, OR. Available online at: Waknitz, F. W., Matthew, G.M., Wainwright, T. and Winans, G.A Status Review for Mid-Columbia Summer Chinook Salmon, NOAA Tchnical Memorandum NMFS-NWFSC- 22. NOAA, Northwest Fisheries Science Center, Seattle, WA. Available online at: Yuen, Henry Personal communication. USFWS Columbia River Fisheries Program Office, Vancouver WA. Draft 2013 Annual Report 158 May 2014

174 VI Columbia River Basin Hatchery Releases of Anadromous Salmon Species A. General Overview of Hatchery Section The Fish Passage Center (FPC) maintains a hatchery database of anadromous salmon species released from State, Federal, and Tribal hatcheries in the Columbia River Basin. This database contains numbers of anadromous hatchery fish released above Bonneville Dam since 1979 and released below Bonneville Dam since The FPC database was upgraded to also facilitate its use for Artificial Production Review and Evaluation (APRE) and Hatchery Genetic Management Plan (HGMP) purposes. For hatcheries releasing fish into the Columbia River Basin, the FPC receives preliminary hatchery release schedules from State, Federal and Tribal agencies prior to the juvenile fish migration. These release schedules are initially entered in the FPC database and then updated on a weekly or monthly basis throughout the year until the release numbers are finalized by the State, Federal, and Tribal fish agencies. Most hatchery releases take place during the spring and summer seasons. Hatchery release data are available for query via the FPC website ( and are used for various purposes throughout the Columbia River Basin. Hatchery release data are also available via the Hatchery Release Mapping Application on the FPC website ( This mapping application allows users to not only obtain hatchery release data, but also generate maps of the release sites, hatcheries, or release rivers of interest. An explanation of the fields used in the FPC hatchery release database can be found on the Metadata website ( Release data from the FPC hatchery release database provide salmon managers with hatchery release information for assessing that year s migration of juvenile hatchery fish through the hydrosystem, which aids in making hydrosystem recommendations during the juvenile passage season. Furthermore, from March to November, the FPC staff uses these data to compile a portion of their weekly reports, which provide a list of all hatchery releases (above Bonneville Dam) 2 weeks prior and 2 weeks after the date of the report. The FPC staff also uses these data to fill more specific data requests regarding present and historical production releases, timing and magnitude of runs, in-season population estimates, or proportion of hatchery fish that Draft 2013 Annual Report 159 May 2014

175 are tagged or clipped. Projects that operate as part of the Smolt Monitoring Program (SMP) also rely on these data to inform their daily operations and in the preparation of their weekly and annual reports, particularly when it comes to identifying potential sources of coded-wire tagged (CWT) or Elastomer tagged fish that are released above and collected by their respective project. For this year s Annual Report, we continue with the tradition of providing maps of the release sites and release data for fall Chinook (Map 6.1), spring Chinook (Map 6.2), summer Chinook and sockeye (Map 6.3), coho (Map 6.4), and summer and winter steelhead (Map 6.5) in all four river zones of the Columbia basin. These maps will be available with the final draft of this annual report, published in August of These maps are specific to releases that outmigrated in The release sites in these maps are indicated by individual codes. An explanation of each of these codes can be found in the metadata section of the FPC website ( The summaries presented in sections B through F of this chapter do not include eggs that might be placed in egg boxes or planted in the gravel, fry releases, or releases of mature adults back to their natal streams. A discussion of these types of releases is provided in Section G. The designation of an egg, fry, or adult release is typically left to the releasing agency and the FPC follows this designation when entering data into the hatchery release database. For the most part, releases of eggs, fry, and adults are relatively small in magnitude compared to the magnitude of smolt or pre-smolt releases. Furthermore, it is difficult to determine to what degree these releases contribute to the out-migrant population in future years. In response to a request from the ISAB, FPC has included a table for each release zone that provides a breakdown of marking information by species. These tables (Tables 6.3, 6.5, 6.7, and 6.10) can be found in Sections C through F of this section of the Annual Report. This marking breakdown is intended to provide insight as to what proportion of the hatchery juveniles released for out-migration in 2013 (excluding eggs and fry) were marked with external (e.g., fin clips, Elastomer tags, floy tags) or internal (e.g., coded-wire tags, blank-wire tags, PIT tags, otolith marks, etc.) marks or tags. It is important to note that, for this summary, unmarked fish are those fish that do not receive any mark at all. Therefore, fish that are marked with internal marks that require special equipment to detect (e.g., coded-wire tags, blank-wire tags, PIT tags) or are not visible until after sacrifice (e.g., otolith marks) were considered marked. As in previous Annual Reports, more detailed marking information is available for each release in Appendix F. The information in Appendix F allows the reader to determine which release groups are marked with internal marks or tags only and may, therefore, be visibly indistinguishable from wild fish. Draft 2013 Annual Report 160 May 2014

176 Fish that fall in the category of non-anadromous by the fish managers are not included in the FPC hatchery release schedule (e.g., subyearling summer Chinook released in Lake Chelan, since these fish normally do not migrate from the lake). Agency-specific databases and/or reports for non-anadromous hatchery releases to the Columbia River Basin are available on the internet. To date, the FPC staff has found two such databases and/or reports: (1) ODFW ( and (2) IDFG ( The 2013 Hatchery Release Schedule (Appendix F) lists the agency, hatchery, and release numbers along with other pertinent data such as detailed marking information, number per pound, date of release, release site, and river zone. The 2013 release data, along with release data from historic years (as far back as 1979) can also be accessed at the FPC Website ( Tables 6.2, 6.4, 6.6, and 6.9 list the hatchery release totals for the below Bonneville Dam ( ), Lower Columbia ( ), Mid-Columbia ( ), and Snake River ( ) zones, respectively. Figure 6.1 provides a time series of the release totals for each of the six species that have been released above Bonneville Dam since In addition, Figures 6.6 to 6.9 provide a time series of available data for each of the individual release zones. A general overview of the 2013 releases is presented in Section B below, followed by a more detailed discussion of the hatchery releases for each river zone (Sections C F). Figure 6.1. Hatchery release totals in Columbia River Basin (above Bonneville Dam) since Draft 2013 Annual Report 161 May 2014

177 B. General Overview of 2013 Releases In 2013, nearly 139 million juvenile salmonids were released from Federal, State, Tribal or private hatcheries into the Columbia River Basin. This release total includes juveniles released both above and Below Bonneville Dam. Of these, just over 85 million (61%) were released above Bonneville Dam while the remaining 53.6 million (39%) were released below Bonneville Dam. Table 6.1 provides hatchery release totals for all four river zones, by species. Table 6.1. Hatchery release totals by River Zone: Snake River, Mid-Columbia River (above McNary Dam), Lower Columbia River (Bonneville Dam to McNary Dam), and Below Bonneville Dam intended for out-migration in Release numbers do not include fry or egg releases intended for out-migration in Race/Species Snake River Mid- Columbia Lower Columbia Below Bonneville Dam Total Release Fall Chinook 5,672,695 11,941,842 21,991,369 26,559,132 66,165,038 Spring Chinook 11,018,463 3,652,328 5,021,414 11,690,871 31,383,076 Summer Chinook 2,858,843 3,620, ,479,008 Coho 963,684 2,522,419 4,422,735 10,961,176 18,870,014 Sockeye 308, , ,206 Summer Steelhead 9,296,442 1,041, ,306 1,996,291 12,821,593 Winter Steelhead ,446 1,821,231 1,875,677 Cutthroat Trout , ,835 Chum , ,004 Total 30,118,213 23,034,428 31,977,270 53,560, ,690, Fall Chinook In migration year 2013, approximately 66.2 million hatchery fall Chinook were released in the Columbia River Basin (Table 6.1). A map of the fall Chinook releases for 2013 outmigration can be found at the end of this chapter (Map 6.1). Hatchery fall Chinook that are released in the Columbia River Basin fall into two basic life-history categories: early fall adult runs (i.e., mostly tules) and late fall adult runs (i.e., mostly brights). Of the 66.2 million fall Chinook juveniles released in migration year 2013, nearly 37.5 million (57%) were fall Chinook tules while the remaining 28.7 million (43%) were fall Chinook brights. Hatchery fall Chinook tules were released only in the Below Bonneville and Lower Columbia River zones. Approximately 65% of the fall Chinook tules released for out-migration in 2013 were released in the Below Bonneville River Zone, while the remaining 35% were released in the Lower Columbia River Zone (Figure 6.2). Hatchery fall Chinook brights were released in all four river zones, with the majority being released above Bonneville Dam in the Lower Columbia (3%), Mid-Columbia (41%), and Snake River zones (20%) (Figure 6.2). Only Draft 2013 Annual Report 162 May 2014

178 about 8% of the fall Chinook brights released in the Columbia River Basin for out-migration in 2013 were released below Bonneville Dam, all of which are released from Bonneville Hatchery. Figure 6.2. Proportion of hatchery fall Chinook (tules and brights) released into each of the four river zones for out-migration in Release numbers do not include egg or fry releases that would out-migrate in Spring Chinook Nearly 31.4 million hatchery spring Chinook were released into the Columbia River Basin for out-migration in 2013 (Table 6.1). This release total includes only releases of parr, presmolts, and smolts and does not include any hatchery releases of spring Chinook fry, eggs, or adults. A map of the hatchery spring Chinook releases for 2013 out-migration can be found at the end of this chapter (Map 6.2). Hatchery spring Chinook were released in all four river zones. As in recent years, approximately 37% of the hatchery spring Chinook that were released for outmigration in 2013 were released in the Below Bonneville River Zone (Figure 6.3). The Lower Columbia and Mid-Columbia river zones represented 16% and 12% of the release total for hatchery spring Chinook in 2013, respectively (Figure 6.3). Finally, about 37% of the hatchery spring Chinook that were released for out-migration in 2013 were released in the Snake River Zone (Figure 6.3). Draft 2013 Annual Report 163 May 2014

179 Figure 6.3. Proportion of hatchery spring Chinook released into each of the four river zones for out-migration in Release numbers do not include egg or fry releases that would out-migrate in Summer Chinook Nearly 6.5 million hatchery summer Chinook were released in the Columbia River Basin for out-migration in 2013 (Table 6.1). A map of the hatchery summer Chinook releases for 2013 out-migration can be found at the end of this chapter (Map 6.3). As in past years, hatchery summer Chinook were released only in the Mid-Columbia and Snake River zones in Of the hatchery summer Chinook juveniles that were released for out-migration in 2013, over 3.6 million (56%) were released in the Mid-Columbia River Zone, while just over 2.85 million (44%) were released into the Snake River Zone. 4. Coho Nearly 18.9 million hatchery coho were released into the Columbia River Basin for outmigration in 2013 (Table 6.1). This release total includes only releases of smolts and does not include any hatchery releases of coho fry or eggs. A map of the hatchery coho releases for 2013 out-migration can be found at the end of this chapter (Map 6.4). Hatchery coho are released in all four river zones. The majority (58%) of hatchery coho were released in the Below Bonneville River Zone (Figure 6.4). The Lower Columbia and Mid-Columbia river zones represented 24% and 13% of the release total for hatchery coho in 2013, respectively (Figure 6.4). The hatchery coho released in the Mid-Columbia Zone are all part of the Yakama Tribal program to reintroduce coho to the Yakima, Methow, and Wenatchee rivers. Finally, about 5% of the hatchery coho released for out-migration in 2013 were released by the Nez Perce Tribe into the Draft 2013 Annual Report 164 May 2014

180 Snake River Zone (Figure 6.4). The percentages attributed to each of the four river zones in 2013 are consistent with what has occurred in recent years. Figure 6.4. Proportion of hatchery coho released into each of the four river zones for out-migration in Release numbers do not include egg or fry releases that would out-migrate in Sockeye A total of 564,206 hatchery sockeye juveniles were released into the Columbia River Basin for migration year 2013 (Table 6.1). This release total includes only releases of pre-smolts or smolts and does not include any hatchery releases of sockeye fry, eggs, or adults. For information on releases of sockeye fry, eggs, and/or adults in 2013, see Section G. Hatchery sockeye smolts and pre-smolts are released only in the Mid-Columbia and Snake River zones. Of the sockeye pre-smolts and smolts released for 2013 out-migration, about 55% were released in the Snake River Zone while 45% were released in the Mid-Columbia River Zone (Table 6.1). A map of the hatchery sockeye releases for 2012 out-migration can be found at the end of this chapter (Map 6.3). 6. Steelhead Nearly 14.7 million hatchery steelhead juveniles were released into the Columbia River Basin for migration year 2013 (Table 6.1). A map of the steelhead releases for 2013 outmigration can be found at the end of this chapter (Map 6.5). There are two life-history categories among hatchery steelhead released in the Columbia River Basin: summer and winter runs. Of the nearly 14.7 million hatchery steelhead released for the 2013 out-migration, about 12.8 million (87%) were summer steelhead while nearly 1.9 million (13%) were winter steelhead. As in previous years, winter steelhead were released only into the Below Bonneville and Lower Draft 2013 Annual Report 165 May 2014

181 Columbia River zones in Of the winter steelhead released for the 2013 out-migration, approximately 97% were released in the Below Bonneville River Zone. The remaining 3% were released into the Lower Columbia River Zone (Figure 6.5). Hatchery summer steelhead juveniles were released in all four river zones in Unlike winter steelhead, the Below Bonneville River Zone only represented 16% of the total summer steelhead release (Figure 6.5). The Lower Columbia and Mid-Columbia river zones represented 4% and 8% of the release total for summer steelhead in 2013, respectively (Figure 6.5). The majority (72%) of the hatchery summer steelhead released in 2013 were released into the Snake River Zone (Figure 6.5). Figure 6.5. Proportion of hatchery summer and winter steelhead released into each of the four river zones for out-migration in Release numbers do not include egg or fry releases that would out-migrate in Cutthroat Trout and Chum The only other species of anadromous salmonids that had hatchery releases for outmigration in 2013 were sea-run cutthroat trout and chum. In all, 117,835 sea-run cutthroat trout and 414,004 chum were released for the 2013 out-migration. Both of these species were released exclusively in the Below Bonneville Dam River Zone (Table 6.1). C. Below Bonneville Dam Zone For the FPC Hatchery Release database, the Below Bonneville Dam Zone is designated as the area from the mouth of the Columbia River to Bonneville Dam, which includes tributaries that empty into the Columbia River below Bonneville Dam. For the 2013 out-migration, just Draft 2013 Annual Report 166 May 2014