Aquatic Habitats and Instream Flows at the Carmen-Smith Hydroelectric Project, Upper McKenzie River Basin, Oregon

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1 Aquatic Habitats and Instream Flows at the Carmen-Smith Hydroelectric Project, Upper McKenzie River Basin, Oregon FINAL REPORT Prepared for Eugene Water & Electric Board Eugene, Oregon Prepared by Stillwater Sciences Arcata, California February 2006

2 Suggested citation: Stillwater Sciences Aquatic habitats and instream flows at the Carmen-Smith Hydroelectric Project, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. i

3 Aquatic Habitats and Instream Flows at the Carmen-Smith Hydroelectric Project, Upper McKenzie River Basin, Oregon EXECUTIVE SUMMARY Introduction The Carmen-Smith Hydroelectric Project (Project) (FERC No. 2242) is a 120-megawatt facility owned and operated by the Eugene Water & Electric Board (EWEB). The Project s existing license, issued by the Federal Energy Regulatory Commission (FERC) under the Federal Power Act, expires 30 November To obtain a new license for operating the Project, EWEB is employing the traditional three-stage licensing process. During the first stage, EWEB prepared and distributed an Initial Consultation Package (ICP) (EWEB 2003). Following release of the ICP, public meetings and study planning sessions were held in Fall 2003 to discuss the operations and potential environmental effects of the Project. Study planning sessions were attended by representatives of non-governmental organizations, tribes, and many governmental agencies, including the United States Fish and Wildlife Service (USFWS), Oregon Department of Fish and Wildlife (ODFW), National Marine Fisheries Service (NMFS, formerly NOAA Fisheries), and United States Department of Agriculture Forest Service (USDA Forest Service). During the study planning, an Aquatics Technical Subgroup (ATS) was formed with representatives from these groups, who worked together to develop a study plan for the Aquatic Habitats and Instream Flows study (Stillwater Sciences 2004a). In addition to the ATS, an Instream Flows Collaborative Team (IFCT) was established in Summer 2004 for the purpose of making ongoing collaborative decisions during the study s implementation. The objectives of this study were to: (1) map riverine and reservoir habitats for analysis species and life stages in the Study Area, and (2) evaluate how changes in a range of flows affect habitat quantity and quality in Project-affected reaches. During development of the Aquatic Habitat and Instream Flows study plan, the ATS developed the following key questions to be addressed in the study: What amount of habitat is available, or potentially available with alterations to instream flows, for critical life stages of analysis species in the Study Area? Within the Carmen and Smith bypass reaches and portions of the reservoirs affected by Project operations, how does habitat availability for the selected life stages of the analysis species vary with changes in flow? This report describes the results of the Aquatic Habitats and Instream Flows study, which was implemented by EWEB through an order issued by FERC (FERC 2003). This technical report describes the methods used in this study and the results of the analysis. Instream flow recommendations will not be presented in this report, but will be addressed in the License Application, due to FERC in November 2006, based on a combination of results from this study and other relicensing studies, including Population Dynamics of Bull Trout and Spring Chinook Salmon (Stillwater Sciences 2006a) and Hydrologic Regimes (Stillwater Sciences 2006b). ii

4 The Study Area encompasses (1) reservoir and stream reaches of the McKenzie River upstream of Trail Bridge Dam to Koosah Falls, including the Sweetwater Creek and Kink Creek tributaries, and (2) reservoir and stream reaches of the Smith River, including upper Smith River upstream of Smith Dam, and Browder Creek. Methods During the development of this study, the IFCT weighed potential benefits, drawbacks, and limitations of various tools and approaches for evaluating aquatic habitat in the Study Area, depending on the key questions to be addressed. For evaluating instream flows in flowing reaches, the IFCT agreed to a habitat criteria mapping approach (criteria mapping). The habitat criteria mapping approach relies on field mapping of available habitat within representative habitat units (e.g., pool, riffle, run) under varying flow conditions for the species and life stages of interest, rather than an approach based on modeling and extrapolation from transects. Due to the high hydraulic complexity of the habitat in the Study Area, the habitat criteria mapping approach was selected by the IFCT as an appropriate and robust tool. From this habitat criteria mapping approach, habitat areas were estimated for analysis species and life stages; the estimated habitat areas were then used in population modeling to determine habitat-based production within a limiting factors framework. The criteria mapping approach involves defining, mapping, and quantifying good habitat for specific life stages of a selected group of analysis species throughout their existing and potential distributions within the Study Area. Criteria used to determine good habitat were based on values in the scientific literature for each species and life stage selected for analysis; criteria were also determined in collaboration with agencies and species experts. Appropriate ranges of values were agreed upon prior to mapping habitat. In regulated reaches, criteria mapping was used to evaluate habitat availability over a range of flows; in unregulated reaches, criteria mapping was used to evaluate the quantity of habitat available during base flows. Habitat polygons for each analysis species and life stage were delineated on aerial photographic maps in the field, and the resulting polygons were digitized to provide area estimates. A pilot mapping effort was conducted on 2 4 November The purpose of the pilot effort was to evaluate the criteria mapping method and review mapping results from different techniques (e.g., two-dimensional modeling, direct observation) prior to employing these methods in the full study. The pilot effort allowed the methods to be tested and provided an opportunity to revise methods and/or criteria prior to implementing the full study. Although similar habitat mapping approaches have been used successfully in other systems, the habitat criteria mapping approach is a relatively new technique for evaluating aquatic habitat availability and instream flows within a hydroelectric relicensing setting. Therefore, in this study, two-dimensional (2D) modeling was used as a companion assessment tool, allowing comparison of the two methods. The 2D modeling was conducted prior to implementing the full study, and results from 2D modeling were used: (1) to inform flow selection in regulated reaches, and (2) to corroborate habitat criteria mapping. Microhabitat fish distribution surveys (direct observation) and repeat mapping (precision mapping) validated the habitat criteria. Results In the lower Carmen Bypass Reach from Trail Bridge Reservoir to Kink Creek, 18 habitat units were identified and divided into 43 sub-units of relatively similar length; 20 sub-units were randomly selected for mapping suitable habitat. In the lower Carmen Bypass Reach, suitable habitat was mapped at four flows (160, 205, 320, and 345 cfs). Habitat availability for nearly all species and life stages was highest at 205 cfs, with the exception of resident trout spawning and iii

5 bull trout adult habitats. No bull trout adult habitat was mapped in the Carmen Bypass Reach. Resident trout spawning habitat availability increased as flows increased and was highest at 345 cfs. In general, juvenile rearing habitat was abundant, resident trout adult and fry habitat was moderately abundant, and spawning habitat abundance was low. In the Smith Bypass Reach, 50 habitat units were identified and divided into 106 sub-units of relatively similar length, of which 13 were randomly selected for mapping. For all guilds, suitable habitat was mapped at five flows (7, 20, 50, 85, 120 cfs) at the 13 sampling sites. As flows increased, estimates of available habitat in the Smith Bypass Reach increased for spawning habitat, decreased for fry rearing habitat, and remained relatively stable for juvenile rearing and resident trout adult. No bull trout adult habitat was mapped in the Smith Bypass Reach. In general, juvenile rearing habitat was abundant, resident trout adult and fry habitat was moderately abundant, and spawning habitat abundance was low. In the upper Carmen Bypass Reach, aquatic habitat was assessed at a range of flow releases by documenting habitat conditions with photographs and video taken at specified photographic locations, measuring habitat characteristics in the field, and identifying the downstream extent of surface flow at the various releases. Eight sites were selected to evaluate how habitat quantity and quality change over a range of flows released from Carmen Diversion Dam. Releases at Carmen Diversion Dam of 0, 10, 50, 160, 250, and 330 cfs were evaluated. Downstream extent of flow ranged from approximately 100 m (328 ft) from Carmen Diversion Dam at 0 cfs to 3,500 m (11,483 ft) at 330 cfs. In unregulated reaches, habitat classification was conducted at Sweetwater Creek, Kink Creek, the McKenzie River upstream of Carmen Diversion Reservoir, the Smith River upstream of Smith Reservoir, and Browder Creek. For Sweetwater Creek, eight habitat units were selected; in Kink Creek, ten habitat units were selected, and in upper Smith River and Browder Creek, 21 habitat units were selected. In unregulated reaches, adult bull trout habitat was not found. Habitat availability in unregulated reaches for bull trout spawning was low, early and late fry rearing was moderate, and juvenile rearing habitat was abundant. For Chinook salmon, habitat availability for adult and spawning was relatively low, fry rearing was moderate, and juvenile habitat was abundant. Resident trout habitat availability for adults was moderate, spawning and fry rearing were low, and juvenile rearing was abundant. Mountain whitefish fry rearing habitat was moderately abundant and juvenile rearing habitat was abundant. Pacific lamprey and western brook lamprey habitat availability for spawning was low and juvenile rearing was only found in Sweetwater Creek. In the three Project reservoirs, adult habitat was generally most abundant, followed by juvenile rearing habitat; fry rearing was the least abundant. Fish habitat availability in the three Project reservoirs was estimated using habitat criteria developed based on associations between fish distribution and physical habitat characteristics within the reservoirs. Fish distribution surveys generally indicated that: (1) most fish occurred in water less than 6 m (20 ft) deep, (2) few fish were present in water greater than 30 feet deep, and (3) no fish occurred deeper than about 30.5 m (100 ft). Direct observation, 2D modeling, and evaluation of precision mapping were used to corroborate the habitat mapping approach and assess accuracy of the methods. Results from these measures suggest that the habitat criteria mapping is a reliable approach for assessing flow habitat relationships in complex streams. Direct observation suggested a strong correlation between fish habitat utilization and habitat mapped using criteria for good habitat. The 2D modeling suggested strong correlation in spatial patterns between the two methods. Evaluation of precision mapping iv

6 indicated an acceptable degree of repeatability. Although flow alterations may influence macroinvertebrate community composition, little effect was apparent on potential juvenile salmonid prey availability. The behavioral/accidental drift approximation ratios for the samples collected in 2005 suggest that salmonid prey availability was very good in the Smith Bypass Reach and in Sweetwater Creek, but very poor in the lower Carmen Bypass Reach. The behavioral/accidental drift ratios from samples collected in 2004 indicate good salmonid prey availability in the Smith River and the Smith Bypass Reach, and in the McKenzie River and lower Carmen Bypass Reach. In 1999, the salmon prey availability index was higher in the Smith Bypass Reach than in the Smith River above Smith Reservoir. v

7 Table of Contents 1 INTRODUCTION Background Purpose and Relationship to Other Studies Key Questions Study Area METHODS Role of the Instream Flow Collaborative Team Selection of Habitat Criteria Selection of species and life stages Review of the scientific literature Selection of good habitat criteria Definition of guilds Validation of habitat criteria in the field Habitat Unit Classification, Sampling Sites, and Flow Selection Classification of habitat units Selection of sites Selection of flows for habitat criteria mapping Mapping of Suitable Habitat Lower Carmen and Smith bypass reaches and unregulated reaches Upper Carmen Bypass Reach Habitat availability in reservoirs Corroboration of Habitat Criteria Mapping Approach in the Smith Bypass Reach and the Lower Carmen Bypass Reach Direct observation Two-dimensional (2D) modeling Evaluating mapping precision Assessment of Flow Effects on Macroinvertebrate Community Characteristics RESULTS Habitat Classification Regulated reaches Unregulated reaches Site Selection Lower Carmen Bypass Reach and Smith Bypass Reach Upper Carmen Bypass Reach Unregulated reaches Habitat Availability in Lower Carmen and Smith Bypass Reaches Bull trout Chinook salmon Resident trout Mountain whitefish...42 vi

8 3.3.5 Pacific lamprey Western brook lamprey Detritus Large woody debris Habitat Availability in Unregulated Reaches Bull trout Chinook salmon Resident trout Mountain whitefish Pacific lamprey Western brook lamprey Habitat Availability in the Upper Carmen Bypass Reach No flow release cfs flow release cfs flow release cfs flow release cfs flow release cfs flow release Habitat Availability in Reservoirs Corroboration of Habitat Mapping Approach Direct observations Two-dimensional (2D) modeling Evaluating mapping precision Flow Impacts on Macroinvertebrate Community Characteristics Autotrophy/heterotrophy index Shredder-riparian index Suspended load index Stability index Juvenile salmonid food index LITERATURE CITED...68 vii

9 Tables Table 1-1. Key questions and report sections in which they are addressed Table 2-1. Participants of the Instream Flows Collaborative Team (IFCT)... 5 Table 2-2. Expert Advisors to the Instream Flows Collaborative Team (IFCT)... 6 Table 2-3. Fish species and life stages proposed by the IFCT for this study Table 2-4. Geomorphic channel classification system used to delineate habitat units in the lower Carmen and Smith bypass reaches and in unregulated reaches Table 2-5. Habitat criteria guidelines used for mapping suitable habitat in the lower Carmen and Smith bypass reaches and in unregulated reaches Table 2-6. Depths of mean velocity measurements Table 2-7. Functional feeding group categorization and food resources Table 2-8. Invertebrate functional feeding group and behavioral drift ratios as surrogates for stream ecosystem attributes Table 3-1. Summary of habitat unit types in the lower Carmen Bypass Reach Table 3-2. Summary of habitat unit types in the Smith Bypass Reach Table 3-3. Summary of habitat unit types in Sweetwater Creek Table 3-4. Summary of habitat unit types in Kink Creek Table 3-5. Summary of habitat unit types in the McKenzie River upstream of Carmen Diversion Reservoir Table 3-6. Summary of habitat unit types in Smith River and Browder Creek upstream of Smith Reservoir Table 3-7. Sites selected for habitat mapping in the lower Carmen Bypass Reach Table 3-8. Sites selected for habitat mapping in the Smith Bypass Reach Table 3-9. Sites selected for habitat mapping in unregulated reaches Table Summary of target and estimated flows during habitat availability mapping in the lower Carmen and Smith bypass reaches in Table Habitat area per reach length used to define relative habitat area abundance categories Table Estimated bull trout available habitat areas for all flows in lower Carmen Bypass Reach Table Estimated bull trout available habitat areas for all flows in Smith Bypass Reach Table Estimated Chinook salmon available habitat areas for all flows in the lower Carmen Bypass Reach Table Estimated Chinook salmon available habitat areas for all flows in Smith Bypass Reach Table Estimated resident trout available habitat areas for all flows in the lower Carmen Bypass Reach Table Estimated resident trout available habitat areas for all flows in the Smith Bypass Reach Table Estimated mountain whitefish available habitat areas for all flows in the lower Carmen Bypass Reach Table 3-19 Estimated mountain whitefish available habitat areas for all flows in the Smith Bypass Reach Table Estimated Pacific lamprey available habitat areas for all flows in the lower Carmen Bypass Reach Table Estimated Pacific lamprey available habitat areas for all flows in the Smith Bypass Reach Table Estimated western brook lamprey available habitat areas for all flows in the lower Carmen Bypass Reach Table Estimated western brook lamprey available habitat areas for all flows in the Smith Bypass Reach viii

10 Table Habitat area per site and LWD loading category in the lower Carmen Smith Bypass Reach Table Summary of flows during habitat availability assessment in unregulated reaches in Table Estimated bull trout available habitat area in Sweetwater Creek Table Estimated bull trout available habitat area in Kink Creek Table Estimated bull trout available habitat area in Smith River above Smith Reservoir and Browder Creek Table Estimated Chinook salmon available habitat area in Sweetwater Creek Table Estimated Chinook salmon available habitat area in Kink Creek Table Estimated Chinook salmon available habitat area in the Smith River above Smith Reservoir and Browder Creek Table Estimated resident trout available habitat area in Sweetwater Creek Table Estimated resident trout available habitat area in Kink Creek Table Estimated resident trout available habitat area in the Smith River above Smith Reservoir and in Browder Creek Table Estimated mountain whitefish available habitat area in unregulated reaches Table Estimated Pacific lamprey available habitat area in unregulated reaches Table Estimated western brook lamprey available habitat area in unregulated reaches Table Summary of target and measured discharges during available habitat area assessment in the upper Carmen Bypass Reach in Table Flow releases at Carmen Diversion Dam for conducting habitat mapping in the lower Carmen Bypass Reach Table Summary of fish habitat utilization in Project reservoirs Table Habitat criteria developed for mapping suitable habitat in reservoirs Table Summary of available habitat area in Trail Bridge Reservoir Table Summary of available habitat area in Smith Reservoir Table Summary of results for the quantitative comparison testing the likelihood that fish observations were within suitable habitat areas mapped (inside-outside test), and the likelihood fish were closer to suitable habitat areas than not (proximity test) Figures Figure 1-1. Figure 1-2. Figure 2-1. Figure 2-2. Figure 2-3. Figure 2-4. Figure 2-5. Figure 2-6. Figure 3-1. Figure 3-2. Relationship of the Aquatic Habitats and Instream Flows study to other Carmen- Smith Hydroelectric Project relicensing studies. Study Area. Photo point locations in the lower Carmen Bypass Reach. Photo point locations in the upper Carmen Bypass Reach. Distribution of cover types used for 2D modeling in lower Carmen and Smith bypass reaches. Macroinvertebrate sampling sites in the Study Area. Inundation zone of Trail Bridge Reservoir and macroinvertebrate sampling using D-frame kicknet within the McKenzie River downstream of Trail Bridge Dam. Field sorting of macroinvertebrates. Annual hydrograph for the lower Carmen and Smith bypass reaches under current conditions based on synthetic hydrologic record from 1 October 1960 to 21 July Life history timing for spring Chinook salmon based on distribution data from the lower Carmen Bypass Reach is indicated above the chart. Available habitat area in the lower Carmen Bypass Reach estimated for bull trout spawning, early fry rearing, late fry rearing, and juvenile rearing. ix

11 Figure 3-3. Available habitat area in the Smith Bypass Reach estimated for bull trout spawning, early fry rearing, late fry rearing, and juvenile rearing. Figure 3-4. Available habitat area in the lower Carmen Bypass Reach estimated for Chinook salmon spawning, fry rearing, and juvenile rearing. Figure 3-5. Available habitat area in the Smith Bypass Reach estimated for Chinook salmon spawning, fry rearing, and juvenile rearing. Figure 3-6. Available habitat area in the lower Carmen Bypass Reach estimated for resident trout adult, spawning, fry rearing, and juvenile rearing. Figure 3-7. Available habitat area in the Smith Bypass Reach estimated for resident trout adult, spawning, fry rearing, and juvenile rearing. Figure 3-8. Available habitat area in the lower Carmen Bypass Reach estimated for mountain whitefish fry rearing and juvenile rearing. Figure 3-9. Available habitat area in the Smith Bypass Reach estimated for mountain whitefish fry rearing and juvenile rearing. Figure Available habitat area in the lower Carmen Bypass Reach estimated for Pacific lamprey spawning and juvenile rearing. Figure Available habitat area in the Smith Bypass Reach estimated for Pacific lamprey spawning and juvenile rearing. Figure Available habitat area in the lower Carmen Bypass Reach estimated for western brook lamprey spawning and juvenile rearing. Figure Available habitat area in the Smith Bypass Reach estimated for western brook lamprey spawning and juvenile rearing. Figure Relative amount of detritus cover types for the trout and char fry rearing guild in habitat units mapped in the Carmen Bypass Reach and the Smith Bypass Reach. Figure Comparison of habitat availability in the lower Carmen Bypass Reach for habitat units having relatively high wood loading to habitat units with relatively low wood loading. Figure Comparison of habitat availability in the lower Carmen Bypass Reach for habitat units having relatively high wood loading to habitat areas mapped during the criteria mapping effort. Figure Comparison of habitat availability in the lower Carmen Bypass Reach for areas in close proximity to wood accumulations to areas not in close proximity to wood accumulations. Figure Estimated available habitat area for analysis species in unregulated reaches. Figure Hydrograph of flow release from the Carmen Diversion Dam for habitat mapping efforts in the Carmen Bypass Reach in May Figure Distance that surface flow extends downstream of Carmen Diversion Dam over a range of flow releases. Figure Downstream extent of surface flows from flow releases in the upper Carmen Bypass Reach. Figure Estimated available habitat area for analysis species and life stages in Trail Bridge Reservoir and Smith Reservoir for the range of low to high pool water surface elevations under current Project operations. Figure Habitat availability for analysis species in Trail Bridge and Smith reservoirs for high and low pool water surface elevations. Figure Comparison of habitat mapping results to 2D modeling results in the lower Carmen Bypass Reach. x

12 Appendices Appendix A. Habitat criteria and guilding summary information. Appendix B. Habitat criteria mapping for regulated reaches. Appendix C. Relative Abundance of Estimated Habitat Areas in the Carmen and Smith Bypass Reaches and Unregulated Reaches. Appendix D. Results of t-tests comparing measured flows in the Carmen and Smith bypass reaches. Appendix E. Video from photo point locations in the Carmen Bypass Reach over a range of flow conditions. Appendix F. Photographs from photo point locations in the Carmen Bypass Reach over a range of flow conditions. Appendix G. Habitat criteria mapping for unregulated reaches. Appendix H. Direct observation results. Appendix I Two-dimensional habitat modeling draft technical report Appendix J. Corroboration of habitat mapping approach: precision mapping. Appendix K. Summary of macroinvertebrate survey results. xi

13 1 INTRODUCTION 1.1 Background The Carmen-Smith Hydroelectric Project (Project) (FERC No. 2242) is a 120-megawatt facility owned and operated by the Eugene Water & Electric Board (EWEB). The Project s existing license, issued by the Federal Energy Regulatory Commission (FERC) under the Federal Power Act, expires 30 November To obtain a new license for operating the Project, EWEB is employing the traditional three-stage licensing process. During the first stage, EWEB prepared and distributed an Initial Consultation Package (ICP) (EWEB 2003). Following release of the ICP, public meetings and study planning sessions were held in Fall 2003 to discuss the operations and potential environmental effects of the Project. Study planning sessions were attended by representatives of non-governmental organizations, tribes, and many governmental agencies, including the United States Fish and Wildlife Service (USFWS), Oregon Department of Fish and Wildlife (ODFW), National Marine Fisheries Service (NMFS, formerly NOAA Fisheries), and United States Department of Agriculture Forest Service (USDA Forest Service). During the study planning, an Aquatics Technical Subgroup (ATS) was formed with representatives from these groups, who worked together to develop a study plan for the Aquatic Habitats and Instream Flows study (Stillwater Sciences 2004a). In addition to the ATS, an Instream Flows Collaborative Team (IFCT) was established in Summer 2004 for the purpose of making ongoing collaborative decisions during the study s implementation, including accommodation of agency participation in field mapping. As issues were raised over the course of the study, EWEB and the ATS or IFCT collaboratively decided how best to proceed. Documentation of issues addressed during the course of the study is available in the FERC record. In 2002, EWEB submitted a plan to FERC for improvements at the Carmen-Smith Hydroelectric Project s Trail Bridge Development saddle dike. EWEB also prepared a draft Biological Assessment (BA) covering the effects of the work at the saddle dike, and the continued operation of the Project, on species listed under the Endangered Species Act. The Biological Assessment also included proposed conservation measures for two of the listed species. FERC adopted the BA and sent it to USFWS and NMFS. In 2003, USFWS and NMFS each filed Biological Opinions with FERC addressing the saddle dike work, continued operation of the Project, and the proposed conservation measures (USFWS 2003, NOAA Fisheries 2003). Also in 2003, FERC authorized the saddle dike work and issued an order approving the conservation measures from the Biological Opinions. USFWS and NMFS s Biological Opinions evaluated the effects of the Project s continued operations under its existing license on listed species, including the Columbia River bull trout Distinct Population Segment (DPS) and Upper Willamette River Chinook salmon Evolutionarily Significant Unit (ESU). These Biological Opinions determined that the continued Project operation and saddle dike work, along with the proposed conservation measures, were unlikely to jeopardize the continued existence of the Columbia River bull trout DPS or Upper Willamette River Chinook salmon ESU. Many of the conservation measures called for studies that would provide information useful for Project relicensing. This technical report describes the results of the Aquatic Habitats and Instream Flows study, which was implemented by EWEB through an order issued by FERC (FERC 2003). This technical report also describes the study s methods and the results of the analysis. Instream flow recommendations will not be presented in this report, but will be addressed in the License Application based on a combination of results from this study and other relicensing studies, including Population Dynamics of Bull Trout and Spring Chinook Salmon (Stillwater Sciences 1

14 2006a) and Hydrologic Regimes (Stillwater Sciences 2006b). Outcomes of the technical studies that pertain to management decisions or actions will be addressed in the License Application, due to FERC in November Purpose and Relationship to Other Studies The quantity, complexity, and quality of riverine habitat available for aquatic species depend to a large extent on instream flows. These flows vary on different temporal scales, and are affected by flow alterations related to Project operations (Stillwater Sciences 2006b). The objectives of this study were to: (1) map riverine and reservoir habitats for analysis species and life stages in the Study Area, and (2) evaluate how changes in a range of flows affect habitat quantity and quality in Project-affected reaches. Analysis species were selected collaboratively with the Instream Flow Technical Collaborative Team (IFCT) and include bull tout (Salvelinus confluentus), Chinook salmon (Oncorhynchus tshawytscha), coastal cutthroat trout (Oncorhynchus clarki clarki), rainbow trout (Oncorhynchus mykiss), brook trout (Salvelinus fontinalis), mountain whitefish (Prosopium williamsoni), Pacific lamprey (Lampetra tridentata), and western brook lamprey (Lampetra richardsoni). The results of this study will be used to evaluate and potential beneficial and negative effects of a range of instream flow on available and potential habitat of analysis species, including any available habitat upstream of Project facilities. Two related studies provided data and analyses used in this study; they are the Fish Population Distribution and Abundance study (Stillwater Sciences 2006c) and the Hydrologic Regimes study (Stillwater Sciences 2006b) (Figure 1-1). Results of the population distribution study were used to refine understanding of the analysis species distributions, which would allow criteria mapping to be focused for each species (i.e., avoiding habitat mapping for species or life stages in locations where they were unlikely to occur). The population distribution study included direct observation and spawning surveys that were used to corroborate habitat criteria for the analysis species. The hydrology study allowed selection of appropriate flow ranges for evaluating the relationships between discharge and habitat availability in the bypass reaches, and for criteria mapping in the unregulated reaches. This study in turn provided data and analyses to two related studies; they are the Population Dynamics of Bull Trout and Spring Chinook Salmon study (Stillwater Sciences 2006a) and the Aquatic Protection, Mitigation, and Enhancement Opportunities study (Stillwater Sciences 2006d) (Figure 1-1). This study provided habitat availability data at selected flows and other input parameters, which were used in population dynamics models developed and run in the Population Dynamics of Bull Trout and Spring Chinook Salmon study (Stillwater Sciences 2006a). The population models assisted in identifying particular habitats or life stages, which could either limit or increase production of bull trout or Chinook salmon populations. This study provided input to the Aquatic Protection, Mitigation, and Enhancement Opportunities study (Stillwater Sciences 2006d), by analyzing the changes in available habitat areas that could result from various enhancement alternatives (e.g., changes in instream flows and fish passage at Trail Bridge Dam). 1.3 Key Questions During development of the Aquatic Habitats and Instream Flows study plan, the ATS developed key questions to be addressed in the study; the key questions are addressed throughout this report (Table 1-1). Note that question 1 refers to both unregulated and bypass reaches, while question 2 refers specifically to bypass reaches. 2

15 Table 1-1. Key questions and report sections in which they are addressed. Key question 1. What amount of habitat is available, or potentially available with alterations to instream flows, for critical life stages of analysis species in the Study Area? 2. Within the Carmen and Smith bypass reaches and portions of the reservoirs affected by Project operations, how does habitat availability for the selected life stages of the analysis species vary with changes in flow? Report section(s) in which key questions are addressed Sections Sections Study Area The Study Area encompasses reservoir and stream reaches of the McKenzie River upstream of Trail Bridge Dam to Koosah Falls, including the Sweetwater Creek and Kink Creek tributaries. The Study Area also encompasses the Smith River upstream of Trail Bridge Reservoir, and reservoir and stream reaches of upper Smith River upstream of Smith Dam including Browder Creek (Figure 1-2). Regulated reaches in the Study Area include the upper and lower Carmen Bypass Reach, and Smith Bypass Reach. Reservoirs in the Study Area include Trail Bridge, Smith, and Carmen Diversion. Unregulated reaches in the Study Area include the McKenzie River upstream of Carmen Diversion Reservoir, Kink Creek, Sweetwater Creek, Browder Creek, and the Smith River upstream of Smith Reservoir. Bunchgrass Creek was not included because a fish barrier lies immediately upstream of its confluence with the Smith Bypass Reach, near the base of Smith Dam. 3

16 2 METHODS This study was implemented in collaboration with the ATS and IFCT. Pursuant to the Aquatic Habitats and Instream Flows study plan (Stillwater Sciences 2004a), Periodic Updates and Decision Points were used to inform participants of issues potentially affecting the study. As issues were raised over the course of the study, EWEB collaborated with the ATS and IFCT to decide how best to proceed. To the extent possible, these issues were resolved with communications such as meetings and s. Decisions were generally unanimous; however, a consensus between all participants was not always reached. Meeting notes that document decisions are available for reference as part of the FERC record. During the development of this study, the ATS weighed potential benefits, drawbacks, and limitations of various tools for evaluating aquatic habitat in the Study Area and selected different approaches depending on the key questions to be addressed. For evaluating instream flows in flowing reaches, the ATS agreed to a habitat criteria mapping approach (criteria mapping) in a meeting on 20 May The habitat criteria mapping approach relies on field mapping of available habitat within representative habitat units (e.g., pool, riffle, run) under varying flow conditions for the species and life stages of interest, rather than an approach based on modeling and extrapolation from transects (e.g., the Physical Habitat Simulation [PHABSIM] model). Due to the high hydraulic complexity of the habitat in the Study Area, the habitat criteria mapping approach was selected by the ATS as a more appropriate and robust tool. Available habitat areas during various flows were assessed only for current reach conditions; changes in channel morphology caused by flow alterations or the addition of instream structures (e.g., large woody debris) over time are likely to result in different flow-habitat relationships. Results from this habitat criteria mapping approach were used to evaluate how changes in a range of flows affect habitat quantity and quality in Project-affected reaches. In addition, results from the habitat criteria mapping provided direct estimates of habitat areas at the flows evaluated for analysis species and life stages under current conditions, which can be used in conjunction with population modeling results for the determination of habitat-based production within a limiting factors framework. In regulated reaches, criteria mapping was used to evaluate habitat availability over a range of flows; in unregulated reaches, criteria mapping was used to evaluate the quantity of habitat available during base flows. The habitat criteria mapping approach involves defining, mapping, and quantifying good habitat (Section 2.2.3) for specific life stages of a selected group of analysis species (Section 2.1.1) throughout their existing and potential distributions (i.e., downstream of natural barriers to migration) within the Study Area. Criteria used to determine good habitat were based on values in the scientific literature for each species and life stage selected for analysis; criteria were also determined in collaboration with agencies and species experts. Habitat criteria values from the scientific literature were reviewed for their applicability to the Study Area, and to the fish populations and assemblages found there. Appropriate ranges of values were agreed upon prior to mapping habitat (Section 2.2.2). Habitat polygons for each analysis species and life stage were delineated on aerial photographic maps in the field, and the resulting polygons were digitized to provide area estimates. A pilot mapping effort was conducted on 2 4 November The purpose of the pilot effort was to evaluate the criteria mapping method and review mapping results using different techniques (e.g., 2D modeling, direct observation) prior to employing these methods in the full study. The pilot effort allowed the methods to be tested and provided an additional opportunity to 4

17 revise methods and/or criteria prior to implementing the full study. Methods for the pilot mapping were similar to those discussed in Section 2.4. Although similar habitat mapping approaches have been used successfully in other river systems (R2 Resource Consultants 2003, McBain and Trush 2003), the habitat criteria mapping approach is a relatively new technique for evaluating aquatic habitat availability and instream flows within a hydroelectric relicensing setting. Therefore, in this study, two-dimensional (2D) modeling was used as a companion assessment tool, allowing comparison of the two methods. The 2D modeling was conducted prior to implementing the full study. In addition, results from 2D modeling were used: (1) to inform flow selection in regulated reaches, and (2) corroborate criteria mapping (Section ). Microhabitat fish distribution surveys (direct observation) and repeat mapping ( precision mapping ) provided validation of habitat criteria. 2.1 Role of the Instream Flow Collaborative Team An Instream Flows Collaborative Team (IFCT) was established in Summer 2004 for the purpose of ongoing collaborative decision-making during the study s implementation. These collaborative decisions included the selection of analysis species and life stages, selection of habitat criteria, definition of guilds, and selection of flows for mapping. Members of the IFCT included participants from the ATS, and species and habitat experts from agencies, academia, and consulting (Table 2-1). Table 2-1. Participants of the Instream Flows Collaborative Team (IFCT). Name Andrew Talabere Catrin van Donkelaar Tim W. Downey Melissa Jundt Stephanie Burchfield Dave Harris Jeffrey Ziller Ken Homolka Rick Kruger Dirk Pedersen Ethan Bell Dr. Sharon Kramer Margaret Beilharz Ramon Rivera Ann Gray Douglas Baus Affiliation EWEB NMFS ODFW Stillwater Sciences USDA Forest Service USFWS In addition to the IFCT, science advisors provided guidance and expert opinion on specific subjects (Table 2-2). 5

18 Table 2-2. Expert Advisors to the Instream Flows Collaborative Team (IFCT). Name Affiliation Expertise Craig Addley Utah State University 2D modeling and instream flows Dr. Colden Baxter Idaho State University Bull trout biology and ecology Dr. Ken Cummins Humboldt State Macroinvertebrate University ecologist Dr. Matthew Dare Boise State University Bull trout ecology and instream flow studies Steve Railsback Dr. Bill Trush Lang, Railsback and Associates McBain and Trush Instream flow studies Habitat mapping methods and instream flow studies 2.2 Selection of Habitat Criteria Habitat criteria for species and life stages selected for analysis were developed to guide the evaluation of suitable habitat availability in the Study Area. The steps used for selecting habitat criteria included (1) selecting analysis species, (2) reviewing the scientific literature, (3) selecting good habitat (4) defining guilds, and (5) validating habitat criteria Selection of species and life stages Proposed analysis species (six salmonid and two lamprey species) and life stages were initially selected, based on comments received from state and federal agencies, and from conservation groups on the Initial Consultation Package (ICP)(EWEB 2003) (Table 2-3). Species and life stages that have similar habitat requirements were later grouped into guilds (Section 2.2.5) for mapping and analysis, as the IFCT determined to be appropriate. A description of fish species present in the Study Area and their distributions are provided in the Fish Population Distribution and Abundance study report (Stillwater Sciences 2006c). Table 2-3. Fish species and life stages proposed by the IFCT for this study. Analysis species Bull trout (Salvelinus confluentus) Chinook salmon (Oncorhynchus tshawytscha) Coastal cutthroat trout (Oncorhynchus clarki clarki) Life stages for analysis Adult Spawning Fry Juvenile Subadult Adult holding Spawning Fry Juvenile Adult Spawning Fry Juvenile 6

19 Analysis species Rainbow trout (Oncorhynchus mykiss) Brook trout 1 (Salvelinus fontinalis) Mountain whitefish (Prosopium williamsoni) Pacific lamprey (Lampetra tridentata) Western brook lamprey (Lampetra richardsoni) 1 Non-native Life stages for analysis Adult Spawning Fry Juvenile Adult Spawning Juvenile Adult Spawning Fry Juvenile Spawning Ammocoete Spawning Ammocoete The final list of analysis species and life stages was identical to the initially proposed ICP list with two exceptions. First, the IFCT decided that the subadult life stage for bull trout could be included in the discussion of adult habitat because of strong similarities in habitat preferences. Second, the IFCT determined that bull trout fry should be split into early fry (< 45 mm) and late fry ( mm) life stages because habitat preferences between these two categories were shown to greatly vary Review of the scientific literature To select habitat criteria values for each analysis species and life stage, the scientific literature was reviewed, and pertinent information was summarized for a wide range of potential habitat criteria. Information was assembled on the following parameters: Water velocity Water depth Substrate size and embeddedness Cover type Distance to nearest cover Channel gradient Water temperature Large woody debris Habitat type Stream size Channel morphology Redd dimensions and egg burial depth (for spawning life stages) Groundwater inflow data (exclusively for bull trout spawning) When available, quantitative information was separated into minimum, maximum, mean, and optimal or preferred values. The habitat criteria values were selected from an extensive literature review, and represented a relatively broad range of values for suitable habitat. Temperature constraints were included in the population dynamics model where appropriate. 7

20 2.2.3 Selection of good habitat criteria Based on the range of values summarized during the literature review, habitat criteria were selected for mapping available habitat, for each analysis species and life stage. The ranges of habitat criteria values considered to represent good habitat were selected collaboratively with the IFCT during a two-day meeting on July 2004, and were based on the habitat criteria values derived from the literature, professional judgment, and site-specific considerations. Good habitat was defined in the study plan as habitat that falls within the range of conditions that the species has evolved to use, at various life stages (i.e., the habitat that provides the conditions allowing successful completion of a species life stage). It does not refer to habitat expected to produce 100% survival or to a narrower subset of preferred conditions that a given life stage may select if presented with the full range of conditions that meet its habitat requirements (Stillwater Sciences 2004a). The habitat criteria selected for this analysis preclude some amount of poor habitat from being included; results from the pilot effort indicated that within the Study Area, conditions typically were characterized by either good habitat or unsuitable habitat (i.e., there was little poor habitat due to very turbulent and fast water and abrupt velocity gradients). Habitat criteria summarized during the literature review were refined to include only studies conducted for species, locations, and using study methodologies considered applicable to the Study Area. Specific criteria selected to define good habitat were also refined based on expert opinion and included: Water depth Water velocity Substrate size Cover type Distance to nearest cover Minimum habitat area Water depth and water velocity were considered key criteria for all analysis species and life stages based on the scientific literature, and were thus the initial criteria to be selected for mapping. Other key criteria were selected only when the characteristic was considered to be fundamental to development, reproductive success, or survival. Good habitat criteria values that were selected by the IFCT for habitat criteria mapping were documented, including comments and rationale for each habitat criteria selection (Table A-1). Temperature was not used as mapping criterion, but temperature constraints were included in the population dynamics model where appropriate. In addition to the habitat criteria listed above, review of scientific literature indicated that upwelling or other physical habitat characteristics may influence bull trout spawning habitat preference in certain localities (Baxter and McPhail 1999, Baxter and Hauer 2000). To determine whether upwelling or some other factor may influence bull trout spawning habitat preference in the lower Carmen Bypass Reach, an assessment of bull trout spawning habitat utilization and preference was developed in collaboration with Dr. Colden Baxter. The sizes and locations of available spawning gravel patches were mapped (using water depth, water velocity and substrate particle size criteria) and habitat where bull trout spawning occurred was delineated in the field onto a base map of the lower Carmen Bypass Reach. These data were digitized into a GIS database to determine whether reach-scale patterns in spawning distribution, relative to habitat availability, could be found (For example, could stream reaches with available habitat, but in which no spawning occurs, be found?). Analyses of GIS data were also used to determine whether factor(s) other than hyporheic or phreatic flows could strongly influence habitat 8

21 characteristics that determine bull trout spawning preferences in this reach. Based on this evaluation, we did not observe spatial patterns indicating that groundwater exchange (e.g., upwelling) or other habitat characteristics were factors in habitat selection by bull trout; thus, groundwater exchange was not included as a criterion for defining suitable habitat. A detailed description of this assessment is provided in Fish Population Distribution and Abundance technical report (Stillwater Sciences 2006c). For mapping purposes, minimum habitat areas (polygons) were selected by the IFCT from literature review and expert opinion for each analysis species and life stage. Minimum polygon sizes for each species and life stage were also summarized (Table A-2) Definition of guilds After selecting good habitat criteria (Section 2.2.3), IFCT members agreed that grouping species and life stages together into guilds would allow more efficient mapping. Guilds consist of species and life stages having similar good habitat requirements. The IFCT determined that bull trout and Chinook salmon habitat criteria would be the primary considerations in the instream flows analysis due to their listing status under the Endangered Species Act. Therefore, criteria for life stages of these species directed the grouping process; criteria for other analysis species were modified when appropriate to facilitate grouping into guilds. The consolidation of species and life stages into guilds was an iterative process. The IFCT developed an initial set of guilds based on literature review, professional judgment, and sitespecific considerations. Guilds were modified based on field application during an intensive field training workshop on September To assist in the guild formation, charts of water depth and water velocity criteria for good habitat were generated for each species life stages (Figure A-1). These charts provided a visual representation of the species, life stage, and guild criteria, and allowed the IFCT to understand and identify the concessions made to individual species life stage criteria during the guild development. The IFCT established eight unique guilds for mapping purposes (Table A-3). Mountain whitefish adult and spawning life stages were originally considered for mapping; however, results from the pilot mapping effort and 2D modeling indicated that habitat availability for these life stages was abundant under current flow conditions compared with other species life stages, and that suitable habitat for all life stages of this species continues to increase with increasing flow. Therefore, the adult and spawning life stages were not included in the final guilds selected for mapping. Mountain whitefish fry and juvenile life stages were included within existing guilds. In addition to the eight fish guilds established, large woody debris (LWD) was considered an important cover element and included as a guild. Based on literature review, the IFCT defined large woody debris as having a minimum size of 10 cm (4 in) diameter and 1 m (3 ft) length as being a commonly used criteria (e.g., Montgomery et al. 1995, Murphy and Koski 1989, Richmond and Fausch 1995), that would provide cover sufficient for fish Validation of habitat criteria in the field Habitat criteria were field-validated in cooperation with the IFCT during the September 2004 training workshop, in which the applications of the selected values to the Study Area were examined. The two-day field training workshop included instruction in measuring habitat criteria and delineating suitable habitat in the field for each species and life stage (e.g., use of flow 9

22 meters, methods for pebble counts). Workshop attendees were all but a few of the members listed in Table 2-1. They were trained in the field mapping methods and then participated in a mapping exercise at one site in the lower Carmen Bypass Reach and one site in the Smith Bypass Reach. Habitat criteria values from the literature and professional judgment of the IFCT were used to adjust some of the selected habitat criteria values. Generally, adjustments were made to facilitate grouping of guilds where relatively minor differences in water depth and water velocity criteria between guilds were evident. The final selection of guilds, including comments on species and life stages for which criteria adjustments were made for incorporation into a particular guild, is given in Table A Habitat Unit Classification, Sampling Sites, and Flow Selection Classification of habitat units The reaches in which habitat units were classified included all flowing stream reaches upstream of project reservoirs to the first likely barrier to upstream migration (for salmonids). Habitat unit classifications were established collaboratively with the IFCT, and were assigned in regulated and unregulated reaches following a modified Hawkins et al. (1993) approach (Table 2-4); this approach uses seven Level II habitat unit types (riffle, turbulent, non-turbulent, pocket water, scour pool, dammed pool, side channel). Sub-units within side channels were also classified as a unique habitat type. Table 2-4. Geomorphic channel classification system used to delineate habitat units in the lower Carmen and Smith bypass reaches and in unregulated reaches (modified from Hawkins et al. 1993). Level I Level II Level III Riffle Low gradient riffle High gradient riffle Fast water Turbulent Fall Cascade Rapid Non-Turbulent Chute Sheet Run Glide Intermediate Pocket Water Scour Pool NA 1 Eddy Trench Mid-channel Convergence Lateral Slow water Plunge Dammed Pool Debris Beaver Landslide Backwater Abandoned Channel Undefined Side channel NA 1 1 No corresponding classification in Level III. 10

23 Habitat units were mapped in the field from downstream to upstream, with sequential numbering of the habitat units starting at the downstream end. Decimals were used to denote side channels or other off-channel units. Habitat unit length, average width, maximum water depth, and channel gradient were recorded for each unit. Level III habitat unit sub-types (Hawkins et al. 1993) were applied and recorded, if applicable, for each unit Selection of sites A stratified random sampling approach was used to select sites for intensive sampling in both regulated and unregulated reaches. Hierarchically, the strata included channel bed morphology, and habitat unit type. Results from sites within each stratum were then extrapolated to similar units within the strata, to estimate available habitat for the reach. River sections were divided into channel types based on channel bed morphologies described by Montgomery and Buffington (1997). The Montgomery and Buffington classification provides a process-based framework in which to assess channel conditions. The different channel bed morphologies provide a meaningful way to categorize reaches that exhibit similar channel characteristics (e.g., channel gradient, channel planform, pool spacing, bed material, and roughness elements). Although channel bed morphology indicates aquatic habitat characteristics, habitat value for fish depends strongly on local conditions. In general, step-pool channels have relatively high gradients (3 6.5%) and frequent turbulent pools; plane-bed channels have moderate gradients (1.5 3%) and few pools; and pool-riffle channels have low gradients (< 1.5%) and moderately frequent pools. Forced pool-riffle channels contain flow obstructions (e.g., large wood accumulations) that force bed morphology, have moderate to low gradients (< 3%), and moderately frequent pools. Maps of channel gradient categories corresponding to Montgomery and Buffington s bed morphologies were generated using GIS software; the maps were then used in the field to validate bed morphology. Where channel bed morphology in the field was different than what appeared on the GIS-produced gradient map, the field-validated morphology was used. Predicted bed morphologies generally matched those observed in the field. The one exception was observed in the High Cascades terrain in the Sweetwater Creek watershed, where plane bed morphology was observed in channels of gradient less than 1.5%, and where pool-riffle (or forced pool-riffle) had been expected. For the purposes of site selection, habitat unit sub-types were grouped into two strata based on slope and flow patterns. Stratum 1 included low-gradient riffle, high-gradient riffle, fall, sheet, cascade, rapid and chute habitats. Stratum 2 included run, glide, pocket water, scour pool (eddy, trench, mid-channel, convergence, lateral, plunge), and dammed pool (debris, beaver, landslide, backwater) habitats Lower Carmen Bypass Reach and Smith Bypass Reach To determine the number of potential sites in the sampling universe, the upstream and downstream limits of the reaches to be sampled were defined based on channel type, fish distribution and utilization, and access and safety, for each regulated reach. In regulated reaches, the extent of habitat units sampled includes: (1) the lower Carmen Bypass Reach of the McKenzie River from Trail Bridge Reservoir upstream to Kink Creek, and (2) the entire Smith Bypass Reach of the Smith River from Trail Bridge Reservoir upstream to Smith Reservoir 11

24 (Figure 1-2). Habitat in the lower Carmen Bypass Reach from Kink Creek to Tamolitch Falls was documented with video and still photography at designated photo points (Figure 2-1). To determine how aquatic habitat is modified with increased flow in the lower Carmen and Smith bypass reaches, a statistical sampling approach was developed. Its purpose was to determine the most appropriate sampling frequency of habitat units for the habitat criteria mapping approach. This method, referred to as the Stepwise Sampling Approach, estimated the appropriate number of sites required to achieve a target level of precision based on sample size and data variance in the field. The target level of precision was set at a 90% confidence interval that is +/- 20% of the total habitat area. During initial mapping efforts, the number of habitat units selected for mapping was estimated by input of a specified precision target level (say, 90%) into a spreadsheet-based statistical program. This target was selected based on a power analysis used to evaluate the relative benefit of increasing sample size and the minimum detectable relative difference in habitat areas among flows. The sample size was initially determined by an evaluation of variance in habitat units based on fish density (in the absence of information on the variability of suitable habitat area). Data collected during the initial mapping effort (which occurred at 205 cfs in the Carmen Bypass Reach and 20 cfs in the Smith Bypass Reach) were analyzed, and the results were used to adjust the number of habitat units necessary to achieve a 20% level of confidence in subsequent mapping efforts. In general, the Stepwise Sampling Approach proceeded as follows: Define the upstream and downstream limits in regulated reaches over which habitat units were sampled. Within these limits, identify the total number of habitat units within each regulated reach. Divide habitat units longer than about 60 m (197 ft) into multiple sub-units of equal lengths (of about 30 m [98 ft]) for sampling purposes. From the total number of habitat units, estimate how many should be sampled at base flow to achieve a target confidence level, estimating variance using fish densities as a proxy for habitat area. Once the number of habitat units are determined, identify the units to be sampled based on stratified random sampling. Select flows greater than base flow, during which to conduct similar sampling. Run statistical procedures (e.g., power analyses) to evaluate the ability to predict and detect differences in habitat area between flows; the two procedures used were a graphical approach and the calculation of Minimum Detectable Relative Differences Unregulated reaches Habitat criteria mapping in unregulated reaches was performed in Sweetwater Creek, Kink Creek, Smith River upstream of Smith Reservoir, and Browder Creek (Figure 1-2). The objectives for evaluating habitat in unregulated reaches were different than those for regulated reaches, and did not require the sampling effort or assessment of variation for the unregulated reaches (i.e., sampling in unregulated reaches was less intensive). The McKenzie River upstream of Carmen Diversion Reservoir was not included because suitable habitat could not be mapped safely due to the steep, confined channel and strong, turbulent flows. 12

25 Unregulated reaches were categorized by geomorphic terrain (i.e., Western Cascades and High Cascades) and channel bed morphology. Kink Creek and Sweetwater Creek are located within High Cascades terrain, and upper Smith River and Browder Creek are located primarily within the Western Cascades terrain. Forced pool-riffle, plane-bed and step-pool channel bed morphologies were identified in the High Cascades terrain; plane-bed and step-pool channel bed morphologies were identified in the Western Cascades terrain. Habitat units that were selected for mapping included reaches located downstream of the first likely barrier (natural or artificial) to upstream migration. In Kink Creek, selected habitat units were limited to those exhibiting surface flow during Spring In Browder Creek, selected habitat units were limited to the lower 942 m (3,091 ft). Habitat units were selected in groups of adjacent habitat units (i.e., representative reaches) to improve efficiency in data collection. An attempt was made to have at least three habitat units within each stratum, for each bed morphology. The reason for selecting a minimum of three or more habitat units per stratum was to allow assessment of variability within the stratum. The locations of groups of units sampled were frequently dependent on the selection of a Stratum 2 habitat unit because they were relatively few in comparison to Stratum 1 habitat units Upper Carmen Bypass Reach Under typical Project operations, the majority of the upper Carmen Bypass Reach remains dry except when Carmen Diversion Dam spills. In the upper Carmen Bypass Reach, sites were selected to evaluate how habitat quantity and quality change over a range of flows released from Carmen Diversion Dam using photo and video documentation and point measurements of wetted channel conditions (width, water depth, and water velocity) (Figure 2-2). Sites were selected to correspond to previously used photo points (Stillwater Sciences 2004b), and to provide relatively even distribution of sites throughout the reach. In addition to monitoring at established sites, the downstream extent of wetted channel was documented at each flow released from the Carmen Diversion Dam Selection of flows for habitat criteria mapping Regulated reaches In regulated reaches, instream flows for conducting habitat criteria mapping were selected with the IFCT. In the lower Carmen and Smith bypass reaches, 2D modeling (Section 2.5.2) was used to inform flow selection. For the lower Carmen Bypass Reach, three flows were initially selected at which to map suitable habitat for all guilds: 150, 200, and 300 cfs. A fourth, intermediate flow of 250 cfs was selected to describe the flow-habitat relationship for guilds most sensitive at intermediate flows (for example, bull trout spawning, Chinook salmon spawning, trout and char fry rearing). Achieving precise flows in the lower Carmen Bypass Reach is difficult due to the lack of control of flow releases at the Carmen Diversion Dam spillway, and the complex geology and subsurface flow patterns in the upper Carmen Bypass Reach. In the Smith Bypass Reach, five flows were selected at which to map suitable habitat for all guilds: 10, 30, 50, 85, and 120 cfs. For each reach, the lowest selected flow approximated summer base flow under current conditions. The primary means used to select intermediate flows were results from 2D modeling. The selection of each high flow was primarily based on the ability of field crews to safely wade 13

26 and measure habitat variables in the reach. Operational constraints were also considered when selecting flows. In the upper Carmen Bypass Reach, complex groundwater flow patterns make prediction of how Carmen Diversion Dam releases will appear as downstream surface flows difficult. Information from a 2003 flow release (Stillwater Sciences 2004b) was used to select flows for this study, based on estimates of downstream extent of surface flow and the lag time between the onset of spill and time of first response. In the upper Carmen Bypass Reach, flows selected to assess habitat availability were 0, 10, 50, and 150 cfs. The 50 and 150 cfs flow releases in the upper Carmen Bypass Reach also coincided with the target flows of 250 and 350 cfs for habitat criteria mapping at the lower Carmen Bypass Reach. In addition to these flows, a 250 cfs flow occurred on 4 May 2005 that was evaluated opportunistically, and a planned spill event of 330 cfs that occurred in October 2003 was also evaluated to the extent possible Unregulated reaches In unregulated reaches, habitat was mapped during Spring Spawning habitat conditions for bull trout and spring Chinook salmon were evaluated during Fall 2005; using professional judgment, to adjust the criteria mapping conducted during spring to reflect suitable habitat under low flow conditions. The USGS McKenzie River at the outlet of Clear Lake gage (# ) and the USGS Smith River upstream of Smith Reservoir gage (# ) provided data used to evaluate flows in unregulated reaches. 2.4 Mapping of Suitable Habitat For each site, a photographic base map was created using low elevation aerial photography (LEAP). Suitable habitat was mapped by delineating good habitat based on habitat criteria developed for analysis species (Table 2-4) in collaboration with the IFCT (see Sections ). Suitable habitat areas that met all of the habitat criteria for a specific guild were delineated on LEAP maps for each site. Detailed descriptions of the habitat criteria mapping approach and analytical methods for assessing available habitat are described below. Table 2-5. Habitat criteria guidelines used for mapping suitable habitat in the lower Carmen and Smith bypass reaches and in unregulated reaches. Guild name Minimum Mean water velocity Total water depth polygon area Cover type and/or Minimum Maximum Minimum Maximum m 2 ft 2 substrate criteria a (m/s) (ft/s) (m/s) (ft/s) (m) (ft) (m) (ft) Adult guilds Bull trout adults NA None None Cutthroat trout adults NA None None Spawning guilds Adult resident trout spawning Bull trout spawning Chinook salmon spawning 0.3 m 2 3 ft 2 D 50 = mm Substrate: ( in) 1.3 m 2 (14 ft 2 ); minimum of 0.9 m (3 ft) wide 1.3 m 2 (14 ft 2 ); minimum of 0.9 m (3 ft) wide Note distance to cover and type Substrate: D 50 = mm ( in) Substrate: D 50 = mm ( in) None None None None None None 14

27 Guild name Trout and char fry rearing Chinook salmon fry rearing Salmonid juvenile Large woody debris Minimum Mean water velocity Total water depth polygon area Cover type and/or Minimum Maximum Minimum Maximum m 2 ft 2 substrate criteria a (m/s) (ft/s) (m/s) (ft/s) (m) (ft) (m) (ft) Fry rearing guilds m cm (4 in) diameter and 1 m (3 ft) length Cover within 0.2 m (0.5 ft) Cover within 0.3 m (1 ft) None None Juvenile rearing guilds Cover within 0.6 m (2 ft); note sandy/silty None None substrate for lamprey Other NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 Unsuitable habitat within a polygon NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 NA 2 Guild Cover types Bull trout spawning Large woody debris, turbulence, depth (> 1.5 m [5 ft]), undercut bank Trout and char fry rearing Detritus (not at criteria at higher flows), small woody debris, grass, sticks, cobble with interstitial spaces, Interstices of cobble and rubble, under boulders, woody debris Trout and char juvenile, and Chinook salmon fry Aquatic and overhead vegetation, woody debris, undercut banks, large unembedded cobble Large woody debris Large woody debris must provide cover or influence the hydraulics of the river Other guilds Woody debris; material that is influencing the hydraulics and/or providing complex cover 1 Velocity is bottom velocity (not mean column velocity). 2 Parameter is not applicable Lower Carmen and Smith bypass reaches and unregulated reaches Low elevation aerial photography and geo-referencing Low elevation aerial photography (LEAP) was obtained by suspending a digital camera from a tethered helium-filled balloon at low altitude (15 46 m [ ft]). The balloon was positioned from the ground and the camera was operated with a wireless remote control. Photographs were taken in a series with approximately 30 50% overlap to ensure a continuous image when compiled. The LEAP images were printed and used in the field to record survey control points. Control points were surveyed with a total station (Sokkia SET 600) and marked on the prints. A minimum of four control points were required for each image. The hard-copy prints marked with the control points were used to geo-reference the LEAP images. To create a spatially accurate representation of each site or reach, the photography was rectified to the surveyed coordinate system. This provided a way to match points on a photograph and other raster-based data to geographic coordinates. While LEAP photos in the Study Area were not referenced to a standardized coordinate system (i.e., State Plane or Universal Transverse Mercator [UTM]), they were referenced to a local coordinate system of control points. Photo 15

28 rectification occurred in the horizontal plane only; topography, camera tilt, and angle distortions were not rectified. After the images for each site were horizontally rectified, the photos were digitally stitched together, creating a composite image that combined all of the rectified images for a site. The composite image was reviewed and the image quality, image order, and edgematching was modified when needed to improve overall quality. The modified, composite images formed the base maps (also called tiles ) for mapping suitable habitat of the various guilds. For each selected habitat unit, LEAP tiles were printed on waterproof paper for field mapping Measurement of stream discharge In lower Carmen and Smith bypass reaches, stream discharge was measured at least once during a given target flow to document actual conditions in the reach. These measurements were used with additional measurements collected as a part of the Hydrologic Regimes study (Stillwater Sciences 2006b) to establish a stage-discharge rating curve. During the high-flow habitat criteria mapping effort, discharge was only measured the first day of mapping, due to safety concerns while wading the cross section. In addition to discharge measurements, water surface elevation data loggers and temporary staff plates were placed at each site, and documented flow conditions at all flows during the study; flows did not appreciably change during habitat criteria mapping. Discharge was measured at designated cross sections adjacent to stage recorders with a minimum of 20 measurements collected along a given cross section. Water depth was measured to the nearest m (0.05 ft) using a top-setting wading rod. Water velocity was measured in ft/s using a Marsh-McBirney (Flowmate 2000) water velocity meter. The depth of a given mean water velocity measurement depended on total depth at the station location (Table 2-5). Table 2-6. Depths of mean velocity measurements. Water depth Depth of velocity measurements m ( 2.5 ft) to 1.5 m (2.5 to 5 ft) ( )/2 > 1.5 m (> 5 ft) ( )/3 1 Depth locations are fractions of total depth as measured from the surface. In the unregulated upper Smith River above Smith Reservoir, stream discharge is monitored at a USGS gage (# ). The location of this gage is 61 m (200 ft) upstream from Smith Reservoir on the right bank, and 1.1 km (0.7 mi) downstream from Browder Creek. On the days during which habitat criteria mapping occurred, average daily discharges in upper Smith River were obtained from the USGS gage. In Sweetwater Creek and Kink Creek, stream discharges were measured approximately one week prior to habitat criteria mapping efforts Estimation of available habitat area Mapping focused on defining the edges of suitable habitat polygons based on the habitat criteria thresholds developed for each guild. Water depth and velocity were measured to define the edges of each polygon, and lines defining the edges were drawn on the LEAP tile for that habitat site. The number of measurements needed to delineate each polygon depended on the size of the polygon and complexity of water depth and velocity patterns. 16

29 In addition to depth and velocity, all rearing guilds and the bull trout spawning guild also incorporated a distance to nearest cover criterion to meet the requirement of a suitable polygon. Cover types were identified visually and minimum horizontal distance to cover was measured. Spawning guilds had the additional habitat suitability parameter of the median particle size (D 50 ) for polygon mapping. For polygons deemed suitable based on other criteria, the D 50 within the polygon was estimated following the Wolman method (1954). Patches where the estimated D 50 fell within the criteria developed by the IFCT were considered suitable. For polygons containing an active redd, the D 50 was estimated by selecting representative particles based on professional judgment so as to not disrupt development of eggs or alevins within the redd. Habitat availability is the estimated amount of habitat in the reach based on suitable habitat areas delineated during habitat criteria mapping. Suitable habitat areas were mapped for a subset of habitat units and then extrapolated to similar habitat unit types within the reach, allowing an estimate of total habitat availability. Therefore, available habitat is defined as the area of good habitat estimated from the extrapolation, based on the subset of habitat unit types that were habitat criteria mapped. For example, if 13 turbulent habitat types exist and five were criteriamapped, the habitat area per unit length for the five units mapped was calculated and applied to the combined length of the remaining eight units, thus generating an estimate of total available turbulent habitat. This type of calculation was performed for all habitat types. The subsets of habitat units selected for criteria mapping are presented in Section 3.2. To assess available habitat in the lower Carmen Bypass Reach, the Smith Bypass Reach, and unregulated reaches, LEAP tiles with available habitat polygons mapped in the field were cataloged and scanned. The scanned images were imported to ArcGIS and georeferenced to the LEAP photo-base using obvious control points. Suitable habitat polygons were then digitized onscreen by tracing over the scanned image. When on-screen digitizing was completed, suitable habitat polygons for every guild in every habitat unit at every flow were given a quality control review to check for digitizing errors, and for any inconsistencies in attribute information. Once the quality control review was completed, suitable habitat areas for each guild were calculated at each combination of habitat unit and flow. These areas were used to extrapolate suitable habitat area to habitat unit within each stratum throughout the reach to estimate overall available habitat area in the reach. Extrapolations were made (1) using a two-stage ratio estimator (Cochran 1977, as cited in Mohr and Hankin 2005) to estimate the guild area per length of stream for each stratum, and then (2) obtaining the total area by multiplying by the length of stream in that stratum. Total guild area and variance were then calculated for the reach by summing the stratum values across all strata. Estimates of guild areas, along with 90% confidence intervals, were then graphed against flow, for each species and life stage to assess flow-habitat relationships. In addition, suitable habitat areas for each species and life stage were standardized by length to facilitate direct comparisons and develop a relative ranking (i.e., relative abundance). Variance was not associated with the area per unit length calculations because it was based only on the habitat units mapped. Relative abundance categorizes the area per unit length calculations, to facilitate description of results. For habitat units mapped, t-tests comparing measured flows at a level of alpha = 0.10 were calculated using a pooled estimate of variance. Estimates of total habitat area and variance per guild were also calculated for unregulated reaches (Sweetwater Creek, Kink Creek, Smith River, and lower Browder Creek) using essentially the same approach as described above. Streambed morphology (e.g., plane-bed, step-pool), in addition to habitat unit strata, were considered. 17

30 An extrapolation was made for upper Browder Creek, where the total suitable habitat area by guild was calculated. We estimated total suitable habitat area for habitat units 20 through 66 by multiplying the estimated mean suitable habitat area per stream area for each guild, based on lower Browder Creek, by the areas of stream within each stratum. The total suitable habitat area by guild from habitat unit 66 upstream to the road crossing barrier was calculated based on the area represented by the known length of stream with an assumed width of 3 m (10 ft), based on field data and reconnaissance. These guild habitat areas were calculated for all species except Chinook salmon. The extent of habitat for Chinook salmon was calculated using stream area data from Smith reservoir to the confluence with Browder Creek. This upstream limit was determined based on investigation of existing habitat conditions (holding and spawning habitat) and professional judgment, and analysis of existing data of Chinook salmon distribution in terms of channel gradient, channel size (bankfull width), and stream order in the McKenzie River and Umpqua River basins (ULEP 1998; ODFW 2002; Stillwater Sciences, unpublished data) Evaluation of relative importance of detritus cover type The detritus cover type was considered to provide potentially greater habitat value for bull trout fry than other cover types in the upper McKenzie River by some members of the IFCT. Therefore, cover provided by detritus within suitable trout and char fry habitat was mapped separately to evaluate the relative amount of cover provided by this cover type over the range of flows mapped. Three types of cover associations with suitable trout and char fry rearing habitats were mapped: (1) habitat where no detritus was present as a cover type, (2) habitat where detritus was mixed with other cover types, and (3) habitat where detritus was the only cover type present. Habitat results for all trout and char fry rearing habitat, regardless of cover type, were included as total habitat area. Using GIS, these three cover types were quantified by reach and by flow and compared. Habitat areas presented in this report represent total area only for those habitat units sampled during the mapping effort (i.e., not extrapolated to the reach) Evaluation of large woody debris effects on suitable habitat area During planning for this study in 2004 and early 2005, the ATS and IFCT recognized that large woody debris (LWD) was to be added to the lower Carmen Bypass Reach as part of a habitat enhancement effort by the USDA Forest Service, with support from EWEB (FERC 2003). The ATS and IFCT scheduled this study s activities to begin prior to the LWD addition. Although large woody debris affects stream hydraulics and habitat availability, the ATS and IFCT members decided to move forward with this study, assuming that addition of LWD would increase habitat similarly at all flows. To determine if LWD additions increase habitat comparably at all flows, two questions were posed: (1) in high-lwd habitat units, would the amount of available habitat at various flows be comparable to amounts of available habitat in low-lwd habitat units, and (2) at various flows, would the amount of habitat in close proximity to LWD be the same as those habitats far from, and therefore not influenced by, LWD? To address the first question, each site was categorized as having either high or low levels of wood loading, based on the total surface area of LWD mapped. Available habitat was calculated separately for habitat units with high and low wood loading, and available habitat per unit length was plotted against flow (high/low test). For the second question, sites with accumulations of LWD were identified and the specific accumulations were selected for analysis. Three-meter (ten-foot) buffers were generated, using GIS, around wood forming the accumulation. The amounts of suitable habitat area within the buffered area, and outside of the buffered area, were calculated, and available habitat per unit length was plotted against flow (proximity test). 18

31 The five guilds proposed in June 2005 and used in the LWD analysis were: Cutthroat adult Bull trout spawning Adult resident trout spawning Trout and char fry rearing Salmonid juvenile rearing The effects of LWD on the relationships between habitat area and flow were first evaluated by calculating mean area per length of stream for habitat units with high-wood loading versus lowwood loading, and then graphing these estimates and the target confidence limit of alpha = 0.1. To address the second question, an analysis of habitat area/flow/lwd relationships was conducted based on buffers drawn around known LWD accumulations. For a given habitat unit and flow, guild area per stream area from inside 3-m (10-ft) buffers was compared to guild area per stream area outside of the buffer. This analysis considers guild areas within the immediate vicinity of LWD to determine whether, and to what extent, LWD influences habitat availability Upper Carmen Bypass Reach The habitat criteria mapping procedure used to quantify habitat in the upper Carmen Bypass Reach was different than the approach described above for the Carmen and Smith bypass reaches, and in designated unregulated reaches. Because this reach was dry part of the year under historical conditions, and is dry most of the year under current conditions, the main objective of mapping in the upper Carmen Bypass Reach was to quantify the amount of stream that becomes wet under varying flow conditions. Releases from Carmen Diversion Dam of 0, 10, 50, 160, 250, and 330 cfs were evaluated. The upper Carmen Bypass Reach could potentially provide habitat for introduced hatchery fish, brook trout, and native cutthroat trout. The downstream extent of wetted channel at each flow release was documented on aerial photographs and with a hand-held GPS unit. All observations were made after spill releases at Carmen Diversion Dam stabilized (~ 2 days). The presence of standing water and backwater habitats at each visit was noted, if present. Wetted width, thalweg water depth, and thalweg water velocity were measured or estimated at each photo point location to document physical changes in channel characteristics if flowing water was present at the time of the visit. Changes in aquatic habitat at the varying flow releases were documented at eight photo points using video and still photography (Figure 2-2). Each photo point was visited during each flow. Photographs were taken upstream, downstream, and across the channel. Video clips approximately 30 seconds long were filmed at each photo point, and notes of the location, date, and any notable changes or features were recorded. During the range of flow releases from Carmen Diversion Dam, aquatic habitat in upper Carmen Bypass Reach was evaluated by: (1) quantifying lineal distance of wetted habitat, (2) identifying locations with standing water, (3) summarizing habitat conditions measured at sites with wetted habitat, and (4) summarizing photo and video taken to document conditions. The downstream extent of surface flow during each flow release was identified on 2004 color orthophotos, and distances downstream of Carmen Diversion Dam were calculated using GIS. 19

32 2.4.3 Habitat availability in reservoirs Within the three Project reservoirs, fish distribution, density, and abundance were quantified based on information from the Fish Population, Distribution, and Abundance study (Stillwater Sciences 2006c) including direct observation surveys (bank and snorkel observations), beach seining, sonar surveys, trapping studies, and a literature review. The literature review on reservoir habitat classification and reservoir habitat utilization by bull trout, Chinook salmon, and cutthroat trout produced very limited information. Habitat preferences of these analysis species were thus assessed by examining fish distribution and density in relation to the reservoirs physical habitat characteristics. Correlations between habitat characteristics and fish abundance were used to define criteria for good habitat in reservoirs. Good habitat for the study was defined as habitat that exhibits the range of conditions that a species has evolved to use at various life stages (see Section 2.2.3). To address key question 1 (Table 1-1) for Project reservoirs, the following objectives were established: (1) describe the reservoir habitats utilized by the life stages of bull trout, Chinook salmon, and cutthroat trout using water depth, substrate, and cover criteria, (2) develop criteria for mapping good habitat within Project reservoirs, and (3) estimate available habitat for each analysis species and life stage for the three Project reservoirs. This approach relies on allowing current fish habitat utilization to dictate the definition of good habitat. Although this approach may overestimate good habitat, it was necessary because information in the scientific literature is insufficient to develop reservoir habitat criteria from literature values. Suitable habitat area for Pacific lamprey and western brook lamprey were qualitatively evaluated in Project reservoirs based on the presence of fine substrate (fine sand and silt). Reservoir habitat criteria were developed by combining information on habitat characteristics and fish habitat utilization from the three reservoirs, using the various survey techniques. Direct sampling was concentrated in Trail Bridge Reservoir due to the presence of bull trout and hatchery-released Chinook salmon. In Trail Bridge Reservoir, habitat characteristics (water depth, substrate, and cover) were delineated on aerial photography with bathymetric contours of the reservoir at low (2,078 ft) and high (2,090 ft) pool. Substrate types (sand/silt, gravel, cobble, boulder, bedrock) and vegetative cover were characterized in areas visible from the water surface (that is, to a water depth of about 10 m [35 ft] at mid to full pool). The portions of Trail Bridge Reservoir that experience daily changes in inundation were also identified. In Smith Reservoir, habitat characteristics were evaluated based on aerial photography, bathymetric maps, and opportunistic observations of substrate and cover types. In Carmen Diversion Reservoir, habitat characteristics were also evaluated based on aerial photography, bathymetric maps, and observations of substrate and cover types. To assess fish habitat utilization in the three Project reservoirs, a number of methods were employed. Trapping studies were conducted in all three reservoirs, and was applied to all three reservoirs. In Trail Bridge Reservoir and Carmen Diversion Reservoir, direct observation surveys were performed. The locations of fish observed were marked on aerial photographs of the reservoirs, and the species and size of each fish were recorded. In Trail Bridge Reservoir, beach seining augmented information from the direct observation surveys. In Smith Reservoir, sonar surveys were conducted to estimate fish distribution and abundance. (Details on the fish survey 20

33 methods are provided in the Fish Population Distribution and Abundance study (Stillwater Sciences 2006c) Habitat criteria and fish distribution data collected in the reservoirs were processed using techniques similar to those used for data collected in the bypass, regulated, and unregulated reaches. Reservoir habitat criteria and fish distribution data were summarized, tabulated, and displayed spatially on reservoir maps. Spatial patterns and/or associations between physical habitat criteria and fish presence and abundance were reviewed within a GIS. If substantial numbers of fish were observed in a specific reservoir area, then that area was generally considered good habitat; habitat in areas where fish were not observed (or rarely observed) were generally considered not to be good habitat. In Trail Bridge and Smith reservoirs, available habitat area was estimated for bull trout (fry, juvenile, sub-adult, and adult), Chinook salmon (fry and juveniles), and cutthroat trout (adult). Fry and juvenile life stages for Chinook salmon were grouped together for available habitat area estimations due to their overlap in habitat utilization. In Carmen Diversion Reservoir, habitat availability was assessed for cutthroat trout (adult). 2.5 Corroboration of Habitat Criteria Mapping Approach in the Smith Bypass Reach and the Lower Carmen Bypass Reach The habitat criteria mapping approach in stream reaches was corroborated with other methodologies to support this approach and to provide a measure of accuracy and repeatability. Three approaches were used: (1) direct observations of fish, to assess their utilization of good habitat, as defined by the guild criteria, and to test the accuracy of the method during pilot mapping, (2) 2D modeling, which provided results that could be compared to the habitat criteria mapping results during pilot mapping, and (3) precision mapping, which provided an evaluation of the repeatability of criteria mapping, during pilot and study mapping. Three sites were selected in collaboration with Craig Addley and the IFCT for mapping in regulated reaches for initial calibration of the proposed field methods; these habitat units also correspond to the three sites for which 2D modeling was conducted Direct observation Direct observation snorkel surveys, as described in Section 2.12 of the Fish Population Distribution and Abundance technical report (Stillwater Sciences 2006c), were used to evaluate whether, and to what extent, fish habitat utilization corresponded to the suitable habitat areas that were mapped in the field, based on guild definitions. Snorkel surveys were conducted on 1 2 November 2004 in one habitat unit in the lower Carmen Bypass Reach and two habitat units in the Smith Bypass Reach; these were the same habitat units selected for 2D modeling and the pilot mapping effort. Though the selection of good habitat was based on information regarding habitat preferences for both the nighttime and daytime, direct observation surveys were conducted during the nighttime to increase the likelihood for making observations (Goetz 1994, Bonneau 1994 as cited in Thurow and Schill 1996, and Jakober 1995). One snorkel survey was conducted in each pilot habitat unit on the night prior to the pilot habitat criteria mapping to reduce the risk of disturbance during the mapping effort, and to ensure that flows and water depths were similar to when habitat criteria mapping occurred. Surveyors worked in an upstream direction, and the location of each observed fish was marked with a unique number on a LEAP tile of the habitat unit. 21

34 Individual fish locations were transferred to GIS using a similar procedure as conducted for the habitat criteria mapping polygons. Photographic tiles with snorkel observation points of the fish locations were scanned, imported to ArcGIS, and georeferenced to the LEAP photo-base. Fish locations were then digitized on-screen. The digitized points were overlaid with suitable habitat area polygons for each guild. The IFCT members used the plots of the snorkel observation points and suitable habitat areas to assess the proximity of snorkel observation points with mapped polygons of suitable habitat area. Quantitatively, two statistical tests were developed to determine whether fish were significantly associated with mapped guild areas: (1) a simple accounting of fish observed inside versus outside the appropriate guild regions ( inside-outside test ), and (2) a consideration of the distance between observed fish and suitable habitat area polygons ( proximity test ). For both tests, the null hypothesis was that the position of each observed fish is a random point in the habitat unit. The first test (inside-outside test) is arithmetically straightforward, but not very powerful; the second test (proximity test) has better power properties, but is computationally more complex Inside-outside test The test statistic, m, is the number of observed fish found strictly inside guild regions. This is significant at the ( 1 α ) 100% confidence level if p < α, where p is the probability that the statistic would be at least as large as the observed value, if fish were distributed according to the null hypothesis (Manly 1997). Under the null hypothesis, m s distribution is represented by: n m n m pr( m n, p) = P (1 P) m where n is the total number of observed fish in the habitat unit and P is the fraction of the total area of the habitat unit areas belonging to the guild regions. The test s weakness is its lack of power; if n is small or P is large, this test may not find any outcome to be significant, and it does not make any concessions for near misses. Its primary utility is its simplicity and robustness, and any positive findings would be especially compelling Proximity test The test statistic SS is the sum of the squares of the distances from each observed fish to the suitable habitat polygon nearest that fish (this distance is zero if the fish is inside a suitable habitat polygon). This statistic is significant at the ( 1 α ) 100% confidence level if p < α, where p is the probability that the statistic would be at least as small as the observed value, if the fish were distributed according to the null hypothesis. The distribution of SS under the null hypothesis is well-defined, but not easy to calculate exactly. It can be approximated to any desired level of accuracy, however, by a straightforward Monte-Carlo algorithm (Manly 1997). The algorithm is: (1) generate a large number B of synthetic data sets under the null hypothesis, (2) evaluate the test statistic for each synthetic data set; the proportion of these values smaller than the observed value will converge to p as B goes to infinity. These calculations were performed in S-Plus, using custom functions for selecting 22

35 random points from polygons, and answering point-in-polygon queries. A minimum of B = 1,000 samples was used to generate the values in this report. The function sm.density from the S-Plus library sm (Bowman and Azzalini 1997) was used to create estimates of the test statistic distribution under the null hypothesis. Plots of the test statistic distributions exhibit thick curves; the thickness is indicative of the variability, showing the uncertainty resulting from the use of Monte-Carlo methods. Results from this test provide an estimate of the degree which fish observations were associated with suitable habitat mapped for that species and life stage based on the criteria Two-dimensional (2D) modeling Two-dimensional (2D) modeling was used to corroborate the habitat criteria mapping approach because 2D modeling is an accepted tool for evaluating hydrodynamic conditions in relatively non-turbulent conditions (LeClrec et al. 1995, Ghanem et al. 1996). During a Summer 2004 IFCT meeting, Craig Addley assisted the IFCT in selecting the 2D modeling reaches. Two sites within the Smith Bypass Reach and one site within the Carmen Bypass Reach were considered appropriate because they were comparatively hydraulically simple. For each of the three sites, the 2D modeling required detailed topographic information and a digital terrain model. To provide roughness and potential spawning gravel inputs to the 2D model, substrate characteristics were classified at each site. Water surface elevations and water velocity profiles were measured to provide site-specific data to the hydraulic models. Cover attributes were delineated on photographic base maps (Figures 2-3a c) and used to model habitat for those species and life stages with a minimum distance to cover criteria. The model used was the River2D model (Steffler and Blackburn 2002). The IFCT selected flows to be used for 2D model inputs; these generally encompassed the range of summer and winter base flows occurring under current and pre-project conditions in these reaches. For the Carmen Bypass Reach and Smith Bypass Reach, fifteen flows were modeled ranging from 100 to 1,000 cfs, and 5 to 200 cfs, respectively. From these modeled flows, habitat suitability results were used to assist in the selection of flows for the full habitat criteria mapping effort in regulated reaches (see Section 2.4) Evaluating mapping precision During the mapping effort, independent crews repeated field mapping to assess the precision and repeatability of the habitat criteria mapping method. The independent crews assessed the same sites under similar flow conditions. These repeat surveys were compared to estimate error in the precision of crews mapping of good habitat. During the pilot effort, repeat surveys were conducted for the two sites in the Smith Bypass Reach (habitat units 7 and 34). These sites were mapped on the first day and again on the third day of the pilot mapping effort by switching crews. Maps with suitable habitat polygons and specifics regarding the location, amount, or suitability of habitat (e.g., pebble count results) were not shared between crews until mapping had concluded, to ensure that crews were mapping independently and were not biased by the mapping conducted by the other crew. Evaluation of mapping precision continued from the pilot to the full habitat criteria mapping effort. Sites selected for repeat surveys during the full effort were criteria mapped for a selected number of guilds. 23

36 Evaluation of mapping precision included summarizing specific guild areas mapped by both the original crew and by a calibration crew in the same habitat unit during the same day, and then comparing these areas using linear regression. Two models were initially tested for fit of original and repeat mapping areas. These models, one using observed area per unit length and the other using log (observed area), were compared by calculating a statistic, Akaike s Information Criterion (AIC), for both. The log (observed area) model had the lowest AIC score (51 compared with a score of 115 for the observed area per unit length model), and was therefore selected to estimate the error between original and repeat habitat criteria mapping areas. The Delta Method (Xu and Long 2005) was applied using the residual standard error of the model to produce a symmetric confidence interval around the mean percent difference of estimated areas between crews. This was done by dividing the residual standard error of the model (0.2614) by the square root of 2, to produce an estimate for the standard deviation of the error in log area between mapping crews. This standard deviation was then multiplied by the appropriate z value (1.6449, for alpha = 0.10) to obtain a 90% confidence interval of ± for observer error. 2.6 Assessment of Flow Effects on Macroinvertebrate Community Characteristics To address the effects of instream flows and flow fluctuations on the macroinvertebrate community in riverine reaches, a 2-day field assessment of the macroinvertebrate community was conducted at selected sites within the Study Area on 9 10 May Dr. Ken Cummins, an established expert on macroinvertebrates and stream ecology, led this field effort. Information gained from this visit was used to evaluate the effects of instream flows on macroinvertebrate habitat quantity and quality, and the effects on any associated higher trophic levels (i.e., fish). Within regulated reaches, two sites were sampled: (1) lower Carmen Bypass Reach (Figure 2-4), and (2) lower Smith Bypass Reach (Figure 2-4). Another site was located in Sweetwater Creek, an unregulated reach, for comparison. Macroinvertebrate sampling was conducted for 30-second periods using a D-frame kick net fitted with a 500-µm (0.02 in) mesh collection net (Figures 2-5a b). Macroinvertebrates residing within stream substrates were sampled by thrusting the kick net into the stream bottom and margins at random locations. Litter deposits were sampled by scooping litter into the net to suspend any organisms within these materials. In fast water moving over cobble-gravel substrates, the sediments were sampled by kicking and dislodging substrate upstream of a sampling net held against the bottom, causing the macroinvertebrates to be dislodged into the net (Hauer and Resh 1996). Samples were thoroughly rinsed from the collection net into a plastic tub. Macroinvertebrates from each location were sorted in the field by functional feeding groups (Figure 2-6) according to the classification system developed by Cummins and Klug (1979), later modified by Merritt and Cummins (1996) (Table 2-6). The separation of macroinvertebrates into functional feeding groups is based on the mechanisms by which they acquire food; the morphological and behavioral adaptations for acquiring food are readily observed in the field with live, freshly collected specimens. Samples were then preserved in 95% ethanol. 24

37 Table 2-7. Functional feeding group categorization and food resources (adapted from Merritt and Cummins 1996). Functional feeding group Shredders Filtering collectors Gathering collectors Scrapers Feeding mechanisms Chew conditioned litter or live vascular plant tissue, or gouge wood Suspension feeders filter particles from the water column Deposit feeders ingest sediment or gather loose particles in depositional areas Graze rock and wood surfaces or stems of rooted aquatic plants Capture and engulf prey or tissue, Predators ingest body fluids 1 CPOM Coarse particulate organic matter. 2 FPOM Fine particulate organic matter. Dominant food resource CPOM 1 decomposing (or living hydrophyte) vascular plants FPOM 2 decomposing detrital particles; algae, bacteria, and feces FPOM 2 decomposing detrital particles; algae, bacteria, and feces Periphyton attached nonfilamentous algae and associated detritus, microflora and fauna, and feces Particle size range of food (mm) > Prey living animals > 0.5 Grouped according to functional feeding groups, the macroinvertebrate community composition data were used to assess ecosystem and habitat attributes of the lower Carmen Bypass Reach, Smith Bypass Reach, and Sweetwater Creek, based on criteria developed by Dr. Cummins (Table 2-7). In addition, the behavioral drift ratio was used as an index of potential salmonid food availability; behavioral drift is the mechanism of dispersal for many macroinvertebrates (essentially all filtering collectors and many of the gathering collectors), making them vulnerable to drift-feeding juvenile salmonids. The relationships between macroinvertebrate community compositions, along with information from additional benthic macroinvertebrate sampling efforts in 1999 and 2004 (see below), were then used by Dr. Cummins to characterize the sites and to determine potential impacts to the macroinvertebrate community associated with Project effects on instream flows. Table 2-8. Invertebrate functional feeding group and behavioral drift ratios as surrogates for stream ecosystem attributes. Ecosystem attribute Autotrophy/ heterotrophy index Shredder-riparian index Suspended load index Description Gross primary production/ total community respiration Benthic CPOM 1 / benthic FPOM 2 FPOM in transport/ benthic FPOM Functional feeding group and behavioral drift ratio Scrapers/(shredders + total collectors); Threshold: >0.75 indicates autotrophy Shredders/total collectors; Threshold: fall-winter >0.50; springsummer >0.25 indicates good shredderriparian linkage Filtering collectors/gathering collectors; Threshold: >1.00 indicates FPOM in transport is high 25

38 Ecosystem Functional feeding group and Description attribute behavioral drift ratio (Scrapers+filtering collectors)/(shredders+gathering Substrate stability collectors); Stability (cobbles and wood) Threshold: >0.60 indicates flows and substrates stable, supporting less mobile taxa (Filtering + gathering Predictable supply collectors)/(scrapers + Juvenile salmonid (behavioral drifters)/ food index 3 shredders+predators); unpredictable supply Threshold: >0.50 indicates potential (accidental drifters) good salmonid food availability 1 CPOM Coarse particulate organic matter. 2 FPOM Fine particulate organic matter. 3 This is an approximation of the juvenile salmonid food intake index based on field data. The actual ratio can only be determined in the laboratory using more detailed taxonomic determinations. Dr. Cummins evaluated macroinvertebrate sample data collected in 1999 by the McKenzie River Watershed Council and USFS (Aquatic Biology Associates, Inc. 1999) and in 2004 by Stillwater Sciences (Stillwater Sciences 2006e) using the same classification system (Table 2-7). Comparisons were made of data taken at sites above diversions (unregulated reaches) and sites below diversions (regulated reaches) to evaluate effects of diverting flow from the Smith and McKenzie rivers. 26

39 3 RESULTS 3.1 Habitat Classification Habitat was classified throughout the Study Area, but is presented in two sections: the regulated reaches (the lower Carmen Bypass Reach and Smith Bypass Reach), and the unregulated reaches (Sweetwater Creek, Kink Creek, the McKenzie River upstream of Carmen Diversion Reservoir, and the Smith River upstream of Smith Reservoir) Regulated reaches Habitat was classified in the lower Carmen Bypass Reach and Smith Bypass Reach. In the lower Carmen Bypass Reach, 3,515 m (11,533 ft) of main channel and 642 m (2,106 ft) of side channel habitat were delineated, for a total of 4,158 m (13,642 ft) of stream channel classified in this reach. All habitat units in the reach were classified as having plane-bed morphology based on channel bed morphologies described by Montgomery and Buffington (1997). Riffles and turbulent habitat unit types were the primary types, comprising 49% and 17%, respectively, of the total area delineated (Table 3-1). Table 3-1. Summary of habitat unit types in the lower Carmen Bypass Reach. Habitat unit types Number of habitat units Total length m ft Total length (%) Total area (%) Plane-bed morphology Riffle 19 1,752 5, Turbulent , Non-turbulent , Pocket water , Scour pool Dammed pool Side channel , Total 51 4,158 13, In the Smith Bypass Reach, 2,923 m (9,890 ft) of main channel and 363 m (1,191 ft) of side channel habitat were delineated, for a total of 3,286 m (10,781 ft) of stream channel classified for this reach. The entire Smith Bypass Reach is a mixed alluvial bedrock reach classified as having step-pool bed morphology. Turbulent and pocket water habitat unit types were dominant, comprising 60% and 17%, respectively, of the total area delineated (Table 3-2). Table 3-2. Summary of habitat unit types in the Smith Bypass Reach. Habitat unit types Number of habitat units Total length m ft Total length (%) Total area (%) Step-pool bed morphology Riffle Turbulent 23 1,891 6, Non-turbulent Pocket water ,

40 Habitat unit types Number of habitat units Total length m ft Total length (%) Total area (%) Scour pool Dammed pool Side channel , Total 56 3,286 10, Unregulated reaches Habitat was also classified in selected unregulated reaches in the Study Area: Sweetwater Creek, Kink Creek, the McKenzie River upstream of Carmen Diversion Reservoir, and the Smith River upstream of Smith Reservoir. In Sweetwater Creek, 927 m (3,041 ft) of habitat were delineated from the mouth upstream to a waterfall that creates a barrier to upstream fish migration. No pool or side channel habitat was classified. Riffle and turbulent habitat unit types were the primary types, totaling 48% (riffle, plan-bed morphology) and 34% (turbulent, step-pool bed morphology) of the total area (Table 3-3). Table 3-3. Summary of habitat unit types in Sweetwater Creek. Habitat unit types Number of habitat units Total length m ft Total length (%) Total area (%) Plane-bed morphology Riffle , Turbulent Non-turbulent Pocket water Scour pool Dammed pool Side channel Step-pool bed morphology Riffle Turbulent , Non-turbulent Pocket water Scour pool Dammed pool Side channel Total 36 1,210 3, In Kink Creek, 163 m (535 ft) of habitat were delineated from the McKenzie River confluence upstream to the first barrier to upstream fish migration. All habitat unit types were characterized by step-pool bed morphology. Turbulent and scour pool habitat types were the most abundant types, comprising 48% and 32%, respectively, of the total area delineated (Table 3-4). 28

41 Habitat unit types Table 3-4. Summary of habitat unit types in Kink Creek. Number of habitat units m Length ft Total length (%) Total area (%) Step-pool bed morphology Riffle Turbulent Non-turbulent Pocket water Scour pool Dammed pool Side channel Total In the McKenzie River upstream of Carmen Diversion Reservoir, 504 m (1,654 ft) of habitat were delineated from 150 m (492 ft) upstream of the Carmen Diversion Reservoir bridge to Koosah Falls. Habitat was classified from the bank because wading in the channel was unsafe. Maximum depth and slope were not recorded for the reach, and no side channel habitat was classified. Similar to the Kink Creek habitat unit types, all were characterized by the step-pool bed morphology. Turbulent and scour pool habitat unit types were the primary types, comprising 41% and 36%, respectively, of the total area delineated (Table 3-5). Table 3-5. Summary of habitat unit types in the McKenzie River upstream of Carmen Diversion Reservoir. Habitat unit types Number of habitat units Total length m ft Total length (%) Total area (%) Step-pool bed morphology Riffle Turbulent Non-turbulent Pocket water Scour pool Dammed pool Side channel Total , In the Smith River and Browder Creek upstream of Smith Reservoir, 7,181 m (23,560 ft) of habitat unit types were classified. Riffle, turbulent, and scour pool unit types (of the plane-bed morphology) were the most common types mapped, comprising over 90% of the total area delineated (Table 3-6). No side-channel habitat was classified. 29

42 Table 3-6. Summary of habitat unit types in Smith River and Browder Creek upstream of Smith Reservoir. Habitat unit types Number of habitat units m Total length ft Total length (%) Total area (%) Forced pool-riffle bed morphology Riffle Turbulent Non-turbulent Pocket water Scour pool Dammed pool Side channel Step-pool bed morphology Riffle Turbulent Non-turbulent Pocket water Scour pool Dammed pool Side channel Plane-bed bed morphology Riffle 18 1,111 3, Turbulent 45 4,418 14, Non-turbulent Pocket water Scour pool , Dammed pool Side channel Total 121 7,181 23, Site Selection Sites were selected for habitat mapping in the lower Carmen Bypass Reach, the Smith Bypass Reach, the upper Carmen Bypass Reach, and the unregulated reaches Lower Carmen Bypass Reach and Smith Bypass Reach In the lower Carmen Bypass Reach, the reach from Trail Bridge Reservoir upstream to Kink Creek was selected for sampling (Figure 1-2). This portion of the bypass reach includes 18 of the 51 total habitat units identified for the entire lower Carmen Bypass Reach (from Trail Bridge Reservoir upstream to Tamolitch Falls). The farthest downstream habitat unit (habitat unit 1) was excluded from the population of potential sampling units because it was within the influence of Trail Bridge Reservoir. (Note: habitat unit 1 contained the largest area of gravel deposits in the reach, with an estimated 145 m 2 [1,561 ft 2 ] of potentially suitable spawning habitat area.) Spawning habitat area associated with this habitat unit was included in the population dynamics modeling (Stillwater Sciences 2006a). For sampling purposes, habitat units longer than about 60 m (197 ft) were divided into multiple sub-units that were generally segmented into approximately 30-m (98-ft) long units when possible. These divisions resulted in 43 potential sampling units in the lower Carmen Bypass Reach between Trail Bridge Reservoir and Kink Creek. Potential sampling units were then divided into two strata, with Stratum 1 consisting of 40 habitat units (23 30

43 low-gradient riffles, 4 high-gradient riffles, and 13 rapids) and Stratum 2 consisting of 3 habitat units (1 pocket water, 1 run, and 1 glide). In the Smith Bypass Reach, 50 main channel habitat units were identified. The units were divided into multiple sub-units for sampling purposes with a target length of about 30 m (98 ft), resulting in 106 potential sampling units. These units were divided into two strata, with Stratum 1 consisting of 69 habitat units (5 low-gradient riffles, 53 rapids, and 11 cascades) and Stratum 2 consisting of 37 habitat units (9 runs, 17 pocket water, and 11 pools). Habitat units were selected randomly from within the two strata, with the exception of the three sites analyzed in the 2D modeling (i.e., in the lower Carmen Bypass Reach, habitat unit 6; and in the Smith Bypass Reach, habitat units 7 and 34), which were selected so that results from the two methods could be directly compared. In addition, at least one unit of each existing habitat type was selected. For the lower Carmen Bypass Reach between Trail Bridge Reservoir and Kink Creek, 19 of the 43 units were randomly selected, representing 44% of the total number of units. Sixteen of the 40 (40%) habitat units in Stratum 1 were selected, and all habitat units in Stratum 2 were selected (Table 3-7). After statistically analyzing the data collected during the first mapping effort, one site (Site 9D) was added to the lower Carmen Bypass Reach sampling area to achieve the appropriate sample size using the methodology described in Section , bringing the number of habitat units selected to 17.. Table 3-7. Sites selected for habitat mapping in the lower Carmen Bypass Reach. Strata Habitat unit subtypes Habitat unit numbers Rapid 2A, 2B, 3A, 3B, and 14A Stratum 1 4A, 4B, 4D, 7B, 7D, Low-gradient riffle 8A, 10A, 13B, and 17C High-gradient riffle 9A, 9C, and 9D Run 16 Stratum 2 Glide 11 Pocket water 6 For the Smith Bypass Reach, 14 habitat units were randomly selected, representing 12% of the total number of units. Six of 68 (9%) habitat units in Stratum 1 were selected, and 8 of 37 (22%) habitat units in Stratum 2 were selected (Table 3-8). After statistically analyzing the data collected during the first mapping effort, the sample size for the Smith Bypass Reach was considered adequate to achieve the target confidence interval; therefore, the number of sites was not adjusted for the Smith Bypass Reach. 31

44 Table 3-8. Sites selected for habitat mapping in the Smith Bypass Reach. Stratum 1 Stratum 2 Strata Habitat unit subtypes Habitat unit numbers Rapid 5, 20A, and 27A Low-gradient riffle 8C Cascade 10B and 39A Run 34 and 37 Pocket water 7, 43A, and 50B Plunge pool 8.1 and 22 Eddy pool Upper Carmen Bypass Reach In the upper Carmen Bypass Reach, eight sites were selected to evaluate how habitat quantity and quality change over a range of flows released from Carmen Diversion Dam (Figure 2-2). Six of the eight selected sites correspond to photo point sites that were previously established to document conditions during a spill event (Stillwater Sciences 2004b). Two additional sites were established to provide a relatively even distribution of sites throughout the reach Unregulated reaches In unregulated reaches, groups of adjacent sites were selected, with the goal of selecting at least three habitat units within each of the two strata, for each bed morphology and geologic terrain. Sites selection was generally driven by the locations of habitat units in Stratum 2 because these were relatively few. For Kink Creek, ten sites were selected, representing 75% of the total number of units; in Sweetwater Creek, eight habitat units were selected, representing 23% of the total number of units; and in upper Smith River and Browder Creek, 21 sites were selected, representing 21% of the total number of units (Table 3-9). Table 3-9. Sites selected for habitat mapping in unregulated reaches. Strata Stratum 1 Stratum 2 Stratum 1 Stratum 2 Stratum 1 Habitat unit subtypes Habitat unit numbers Kink Creek Low-gradient riffle 7 and 15 Cascade 5, 10, and 13 Pocket water 11and 12 Plunge Pool 4, 6, and 14 Sweetwater Creek Low-gradient riffle 8, 10, 12, and 18 Cascade 19 Run 9 and 11 Plunge pool 20 Smith River above Smith Reservoir Low-gradient riffle 4 and 14 High-gradient riffle 10, 25, and 41 Rapid 40 Cascade 3, 12, and 16 32

45 Strata Stratum 2 Stratum 1 Stratum 2 Habitat unit subtypes Habitat unit numbers Run 11, 15, and 42 Pocket water 26 Lateral pool 13 and 39 Mid-channel pool 5 Browder Creek Low-gradient riffle 3 High-gradient riffle 5 Rapid 2 Run 6 Lateral pool Habitat Availability in Lower Carmen and Smith Bypass Reaches Available habitat area was estimated to answer the first key question of this study, What amount of habitat is available, or potentially available with alterations to instream flows, for critical life stages of analysis species in the Study Area? For each analysis species and each life stage, a table of the estimated available habitat area at each flow was generated. For current Project operations in the lower Carmen and Smith bypass reaches, an average annual hydrograph was compared with bull trout and spring Chinook salmon life history timing (Figures 3-1a b). Target flows were those selected by the IFCT (Section 2.3.3); during the habitat criteria mapping, actual and target flows were generally consistent, with the exception of the 250 cfs target flow for the Carmen Bypass Reach (Table 3-10). Mapping in the Carmen Bypass Reach during the 250 cfs target flow was conducted opportunistically during the recession limb of a spill event that was not specifically controlled (i.e., flow was not maintained at a specified level for a set period as had occurred for the other mapping efforts); thus, achieving the 250 cfs target discharge proved more difficult. Table Summary of target and estimated flows during habitat availability mapping in the lower Carmen and Smith bypass reaches in Location Lower Carmen Bypass Reach Smith Bypass Reach Target flow Estimated flow 1 Spill at dam 2 (cfs) (cfs) (cfs) Mapping dates July April May May July April April April April 1 Discharge estimated from stage-discharge rating curve for the lower Carmen Bypass Reach (lower site) temporary pressure transducer (Stillwater Sciences 2006b). 2 For lower Carmen Bypass Reach, spill is estimated from Carmen Diversion Dam. For Smith Bypass Reach, spill is estimated from Smith Dam. Spill at dam is the average daily spill value for the assessment date(s). 33

46 In the Carmen Bypass Reach, habitat mapping occurred at discharges ranging from 160 to 345 cfs. The 160 cfs (July) and 205 cfs (April) flows were consistent with average monthly flows that occur in this reach under current conditions for the months of July November (Stillwater Sciences 2006b, Section and Figure 3-11). The higher mapping flows of 320 cfs and 345 cfs were close to, though slightly higher than, typical monthly average flows encountered in this reach under current conditions during the remainder of the year (December June), which range from 250 to 350 cfs. The average annual flow at the downstream end of this reach is about 240 cfs. Average monthly flows in the Carmen Bypass Reach under pre-project conditions are estimated to be roughly 550 to 1,000 cfs (Stillwater Sciences 2006b, Section and Figure 3-11), which were much greater than any of the mapping flows. In the Smith Bypass Reach, habitat mapping occurred at discharges that approximated flows under both pre- and current conditions (Stillwater Sciences 2006b). The 7 cfs flow is similar to the current condition monthly average flow for the months of July October; this flow is also similar to the pre-project condition monthly average flow for August and September. The average monthly flows in November June under current conditions, and in July and October under pre-project conditions, are between cfs, which are represented by the 20 cfs mapping effort. The highest mapping flow in the Smith Bypass Reach was 120 cfs, which is similar to the 105 cfs pre-project condition annual average flow. However, pre-project monthly average flows for December through May were slightly higher than the 120 cfs mapping flow. For each analysis species and its life stages, graphs of available habitat versus flow were used to answer the second key question, How does habitat availability for the selected life stages of the analysis species vary with changes in flow? To interpret the graphs, a number of observations were considered: (1) the pattern of available habitat area versus flow, individually and in comparison with the other life stage graphs for that species and location; (2) whether the available habitat areas at varying flows were significantly different from each other for an individual species and life stage; and (3) whether the pattern was expected or seemed reasonable, based on field observations and professional judgment. The data in the graphs of available habitat can be used to estimate habitat availability throughout the year by comparing the annual hydrograph under current conditions with the life history periodicity for the species of interest (e.g., Figures 3-1a for bull trout and 3-1b for spring Chinook salmon). For example, juvenile Chinook salmon rearing occurs from July through May. Under current conditions, flows in the summer (August October) are generally about 160 cfs, providing approximately 4,050 m 2 (43,594 ft 2 ) of habitat. If flows were increased to 205 cfs during this time, one would expect juvenile rearing habitat availability to increase to approximately 4,780 m 2 (51,451 ft 2 )for that period. Population dynamics modeling (Stillwater Sciences 2006a) was also considered when evaluating habitat availability (e.g., if habitat does not limit a life stage, increasing or decreasing that habitat would not likely affect the population). As stated earlier in this document, instream flow recommendations will not be presented in this report, but will be addressed in the License Application, based on a combination of results from this study and other relicensing studies, including the Population Dynamics of Bull Trout and Spring Chinook Salmon (Stillwater Sciences 2006a), Hydrologic Regimes (Stillwater Sciences 2006b), and Water Quality (Stillwater Sciences 2006e). In the lower Carmen Bypass Reaches, suitable habitat was mapped in 20 habitat units at four flow releases over 13 days; in the Smith Bypass Reach, suitable habitat was mapped in 14 habitat units at five flow releases over 11 days (Appendix B). Suitable habitat in both bypass reaches was mapped for all guilds at all flows, with the exception of the opportunistically sampled 250 cfs flow in the lower Carmen Bypass Reach, for which only 3 guilds (bull trout spawning, Chinook 34

47 salmon spawning, and trout and char fry rearing) were mapped. Available habitat was estimated for each species and life stage mapped at each flow, and the variance associated with each estimate (i.e., 90% confidence interval) was calculated. Suitable habitat areas from mapped units were used to calculate habitat area per unit length in the Carmen and Smith bypass reaches and in unregulated reaches (Appendix C). Available habitat reported in Appendix C is the mapped suitable habitat area standardized by length. Results of t-tests comparing measured flows in the lower Carmen and Smith bypass reaches, for each analysis species and life stage, are presented in Appendix D. Video and still photography document habitat characteristics at designated photo points in the lower Carmen Bypass Reach, from Tamolitch Falls to Kink Creek (Appendices E and F). These standardized available habitat values were then categorized to describe relative habitat area abundance (i.e., relative abundance) to facilitate comparison of habitat available to species and life stages between reaches. For these comparisons, habitat abundance is relative to the maximum value observed (343 m 2 /100 m). Categories defining relative abundances describe relative amount of habitat per unit length (Table 3-11). Table Habitat area per reach length used to define relative habitat area abundance categories. Relative abundance category Relative abundance (%) Habitat area (m 2 /100m) Habitat area (ft 2 /100ft) Very high > 90% > 309 > 1,011 High ,011 Moderate Low Very low < 10% < 34 < Bull trout Lower Carmen Bypass Reach In the lower Carmen Bypass Reach, available habitat area was estimated for the five bull trout life stages (adult, spawning, early and late fry rearing, and juvenile rearing) at three flows (160, 205, and 345 cfs); spawning and early fry rearing were also mapped at 320 cfs (Table 3-12, Figures 3-2a d). Habitat areas for bull trout spawning, fry, and juvenile life stages were greatest at 205 cfs and generally exhibited similar flow-habitat relationships, although amplitudes and relative areas varied. No suitable adult bull trout habitat was found in the lower Carmen Bypass Reach (Table 3-12). Based on the selected habitat criteria, the lack of suitable water depth for adult bull trout restricted habitat availability for this life stage. The lack of suitable adult bull trout habitat was corroborated by PIT tag detections and snorkel surveys conducted for the Fish Population Distribution and Abundance study (Stillwater Sciences 2006c) which indicate that adult bull trout do not use the lower Carmen Bypass Reach outside of the spawning period. All assessments of bull trout habitat were made independent of a temperature criterion. 35

48 Table Estimated bull trout available habitat areas for all flows in lower Carmen Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Adult Spawning 1 Early fry rearing Late fry rearing Juvenile rearing 160 cfs 0 71 (± 25) 833 (± 153) 2,081 (± 327) 4,054 (± 642) 205 cfs (± 36) 931 (± 140) 2,397 (± 370) 4,780 (± 809) 320 cfs NA (± 39) 672 (± 116) NA 2 NA cfs 0 58 (± 33) 555(± 133) 2,103 (± 228) 4,031 (± 411) Estimated available habitat area in ft 2 (90% confidence interval) Flow Adult Spawning 1 Early fry rearing Late fry rearing Juvenile rearing 160 cfs (± 269) 8,966 (± 1,647) 22,400 (± 3,520) 43,637 (± 6,910) 205 cfs 0 1,722 (± 388) 10,021 (± 1,507) 25,801 (± 3,983) 51,451 (± 8,708) 320 cfs NA 2 1,163 (± 420) 7,233 (± 1,249) NA 2 NA cfs (± 355) 5,974 (± 1,432) 22,637 (± 2,454) 43,389 (± 4,424) 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the variability in patch size. 2 Suitable habitat area for this life stage was not measured. Suitable habitat for spawning was generally located along the stream margins and downstream of mid-channel flow obstructions where gravel deposits occurred; gravel patches were generally small and infrequent, and relative habitat area remained very low over the range of flows sampled (Table C-1). Suitable substrate was generally less available than water depth or water velocity. Spawning habitat area was highest at 205 cfs. The habitat area at 205 cfs was significantly different from habitat areas at 160 and 345 cfs, at a level of alpha = 0.10 (Table D-1). The amount of available habitat for bull trout early fry and late fry rearing remains relatively stable as flows increase (Figures 3-2b c). Water velocity generally restricted the amount of suitable habitat for these life stages and, therefore, suitable habitat was located almost exclusively along stream margins. Relative habitat area was low for early fry rearing and moderate for late fry rearing (Table C-1). Although bull trout early fry rearing habitat appears relatively stable as flows increase, available habitat at 160 cfs was significantly different from that at 345 cfs, and available habitat at 205 cfs was significantly different from available habitat area at 320 and 345 cfs, at a level of alpha = 0.10 (Table D-1). Late fry rearing habitat for bull trout was not significantly different at any of the flows mapped, at a level of alpha = 0.10 (Table D-1). For juvenile bull trout, suitable habitat was extensive due to the relatively wide range of suitable habitat criteria values; suitable habitat generally shifted from extending across the channel at lower flows to being concentrated along the channel margins at higher flows. Suitable water velocity was generally less available than other habitat variables. Relative habitat area for juvenile bull trout rearing was very high (Table C-1), with no significant differences between available habitat areas at varying flows, at a level of alpha = Smith Bypass Reach In the Smith Bypass Reach, available habitat area was estimated for five bull trout life stages (adult, spawning, early and late fry rearing, and juvenile rearing) at five flows (7, 20, 50, 85, and 120 cfs) (Table 3-13, Figures 3-3a d). No single flow provided the greatest habitat areas at all life stages. The largest habitat area for spawning was at 120 cfs; fry habitat area was greatest at 7 36

49 cfs; and juvenile rearing habitat area was greatest at 50 cfs (Table 3-13). No suitable habitat for adult bull trout was found in the Smith Bypass Reach (Table 3-13). The lack of suitable water depth for adult bull trout restricted habitat availability for this life stage. All assessments of bull trout habitat were made independent of a temperature criterion. Table Estimated bull trout available habitat areas for all flows in Smith Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Adult Spawning 1 Early fry rearing Late fry rearing Juvenile rearing 7 cfs 0 7 (± 11) 3,397 (± 1,225) 8,135 (± 3,193) 7,000 (± 2,582) 20 cfs 0 22 (± 46) 2,753 (± 1,291) 4,565 (± 1,698) 5,650 (± 1,684) 50 cfs 0 13 (26) 1,737(± 919) 4,829 (± 1,946) 7,587 (± 2,421) 85 cfs 0 31 (± 41) 1,244 (± 912) 4,002 (± 1,401) 6,641 (± 2,154) 120 cfs (± 119) 1,123(± 576) 3,378 (± 1,019) 6,091 (± 1,959) Estimated available habitat area in ft 2 (90% confidence interval) Flow Adult Spawning 1 Early fry rearing Late fry rearing Juvenile rearing 7 cfs ,565 87,564 75,347 (± 118) (± 13,186) (± 34,369) (± 27,792) 20 cfs ,633 49,137 60,816 (± 495) (± 13,896) (± 18,277) (± 18,126) 50 cfs ,697 51,979 81,666 (± 280) (± 9,892) (± 20,947) (± 26,059) 85 cfs ,390 43,077 71,483 (± 441) (± 9,817) (± 15,113) (± 23,185) 120 cfs 0 1,518 12,088 36,360 65,563 (± 1,218) (± 6,200) (± 10,968) (± 21,087) 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the variability in patch size. Similar to bull trout spawning habitat area in the lower Carmen Bypass Reach, suitable habitat for spawning in the Smith Bypass Reach was generally located along the stream margins and downstream of mid-channel flow obstructions where gravel deposits occurred. Suitable gravel patches were generally small and infrequent, and relative habitat area remained very low over the range of flows sampled (Table C-2). Spawning habitat for bull trout generally increased as flows increased, with the greatest increase occurring between 85 and 120 cfs (Figure 3-3a). Bull trout spawning habitat at 7 and 50 cfs were significantly different from the available habitat area at 120 cfs, at a level of alpha = 0.10 (Table D-2). Suitable habitats for early fry and late fry rearing were located almost exclusively along stream margins. Habitat area for bull trout early fry and late fry rearing generally decreased as flows increased (Figures 3-3b c). For bull trout late fry, the greatest decrease occurred between 7 and 20 cfs. Relative habitat area for early fry rearing ranged from low to moderate, and was moderate for late fry rearing (Table C-2). For early fry rearing, habitat area at 7 cfs was significantly different from habitat areas at 50, 85, and 120 cfs; habitat area at 20 cfs was significantly different from habitat area at 85 and 120 cfs, at a level of alpha = 0.10 (Table D-2). For late fry rearing, habitat area at 7 cfs was significantly different from habitat areas at 20, 85, and 120 cfs, at a level of alpha = 0.10 (Table D-2). 37

50 Suitable habitat for juvenile bull trout generally extended across the channel, but at higher flows, habitat was concentrated along the channel margins. Relative habitat area for juvenile bull trout was moderate (Table C-2). Available habitat area remained relatively stable (Figure 3-3d) with no significant differences between available habitat areas at varying flows, at a level of alpha = 0.10 (Table D-2) Chinook salmon Lower Carmen Bypass Reach For Chinook salmon, available habitat area was estimated for four life stages (adult, spawning, fry rearing, and juvenile rearing) at three flows (160, 205, and 345 cfs); available habitat area for spawning was also mapped at 320 cfs (Table 3-14, Figures 3-4a c). Available habitat areas for Chinook salmon spawning, fry, and juvenile life stages were greatest at 205 cfs and generally exhibited similar flow-habitat relationships (Figures 3-4a c). No suitable adult Chinook salmon habitat was found in the lower Carmen Bypass Reach (Table 3-14). The lack of suitable water depth for adult spring Chinook salmon in this reach restricted habitat availability for this life stage. Table Estimated Chinook salmon available habitat areas for all flows in the lower Carmen Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Adult Spawning Fry rearing Juvenile rearing 160 cfs 0 67 (±26) 2,081 (±327) 4,054 (±642) 205 cfs (±36) 2,397 (±370) 4,780 (±809) 320 cfs NA 1 92 (±40) NA 1 NA cfs 0 58 (±33) 2,103 (±228) 4,031 (±411) Estimated available habitat area in ft 2 (90% confidence interval) Flow Adult Spawning Fry rearing Juvenile rearing 160 cfs (±280) 22,400 (±3,520) 43,637 (±3,610) 205 cfs 0 1,551 (±388) 25,801 (±3,983) 51,451 (±8,708) 320 cfs NA (±431) NA 1 NA cfs (±355) 22,637 (±2,454) 43,389 (±4,424) 1 Suitable habitat area for this life stage was not measured. For spawning, suitable habitat was generally located along the margins and downstream of midchannel flow obstructions where small gravel deposits occurred. The lack of suitable substrate generally restricted the amount of available spawning area. Relative habitat area for Chinook salmon spawning was very low (Table C-3), although more spawning habitat was available in the lower Carmen Bypass Reach than in the Smith Bypass Reach. Available habitat area for spawning at 205 cfs was significantly different from available habitat areas for spawning at 160 and 345 cfs, at a level of alpha = 0.10 (Table D-3). For Chinook salmon fry rearing, water velocity generally restricted the amount of suitable habitat and, therefore, suitable habitat was located almost exclusively along stream margins. Relative habitat area for fry rearing was moderate (Table C-3). There were no significant differences in available habitat areas for fry rearing between flows, at a level of alpha = 0.10 (Table D-3). 38

51 For Chinook salmon juveniles, suitable habitat generally shifted from extending across the channel to being concentrated along the channel margins as flow increased. Suitable water velocity generally restricted the amount of suitable habitat. Relative habitat area for juvenile rearing ranged from high to very high (Table C-3). There were no significant differences in available habitat areas for juvenile rearing between flows, at a level of alpha = 0.10 (Table D-3) Smith Bypass Reach In the Smith Bypass Reach, for Chinook salmon, available habitat area was estimated for three life stages (spawning, fry rearing, and juvenile rearing) at five flows (7, 20, 50, 85, and 120 cfs) (Table 3-15, Figures 3-5a c). No single flow appeared to provide the greatest available habitat area for all life stages. No suitable habitat for adult Chinook salmon was found in the Smith Bypass Reach (Table 3-15). For adult Chinook salmon, water velocity generally restricted the amount of suitable habitat. Table Estimated Chinook salmon available habitat areas for all flows in Smith Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Adult Spawning 1 Fry rearing Juvenile rearing 7 cfs 0 0 8,135 (± 3,193) 7,000 (± 2,582) 20 cfs 0 22 (± 46) 4,565 (± 1,698) 5,650 (± 1,684) 50 cfs 0 13 (± 26) 4,829 (± 1,946 7,587 (± 2,421) 85 cfs 0 13 (± 26) 4,002 (± 1,401) 6,641 (± 2,154) 120 cfs 0 82 (± 79) 3,378 (± 1,019) 6,091 (± 1,959) Estimated available habitat area in ft 2 (90% confidence interval) Flow Adult Spawning 1 Fry rearing Juvenile rearing 7 cfs ,564 (± 34,369) 75,347 (± 27,814) 20 cfs (± 495) 49,137 (± 18,277) 60,816 (± 18,126) 50 cfs (± 280) 51,979 (± 20,947) 81,666 (± 26,059) 85 cfs (± 280) 43,077 (± 15,113) 71,483 (± 23,185) 120 cfs (± 850) 36,360 (± 10,968) 65,563 (± 21,087) 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the variability in patch size. For spawning, suitable habitat was generally located along the margins and downstream of midchannel flow obstructions where small gravel deposits occurred. The patchiness of suitable substrate and the variability in patch size often resulted in a large confidence interval for the estimate of spawning habitat area. Suitable substrate was generally more restrictive than other habitat criteria. No spawning habitat was identified at 7 cfs, and the greatest amount was identified at 120 cfs. Relative habitat area for Chinook salmon spawning was very low (Table C- 4). Available habitat area for spawning at 7 cfs was significantly different from available habitat area for spawning at 120 cfs, at a level of alpha = 0.10 (Table D-4). For Chinook salmon fry rearing, water velocity generally restricted the amount of suitable habitat and, therefore, suitable habitat was located almost exclusively along stream margins. Available habitat area for spring Chinook salmon fry rearing generally decreased as flows increased, with the greatest decrease occurring from 7 cfs to 20 cfs (Figure 3-5b). Relative habitat area for fry rearing was moderate (Table C-4). Available habitat area for spring Chinook salmon fry rearing 39

52 at 7 cfs was significantly different from available habitat areas at 20, 85, and 120 cfs, at a level of alpha = 0.10 (Table D-4). Suitable habitat for spring Chinook salmon juvenile rearing generally extends across the channel, but at higher flows, habitat was concentrated along the channel margins. Relative habitat area for juvenile rearing was moderate (Table C-4). Available habitat area remained relatively stable (Figure 3-5d) with no significant differences between available habitat areas at varying flows, at a level of alpha = 0.10 (Table D-4) Resident trout Lower Carmen Bypass Reach For resident trout (cutthroat trout, rainbow trout, and brook trout) in the lower Carmen Bypass Reach, available habitat area was estimated for four life stages (adult, spawning, fry rearing, and juvenile rearing) at three flows (160, 205, and 345 cfs). Fry rearing was also mapped at 320 cfs (Table 3-16, Figures 3-6a d). The patterns of available habitat areas versus discharges were similar for all life stages except for spawning, with the greatest available habitat areas at 205 cfs. Suitable habitat for adult resident trout was generally near the channel margins and downstream of mid-channel flow obstructions. Available habitat area for adult resident trout was highest at 205 cfs (Figure 3-6a), and relative habitat area for adult resident trout was moderate at all flows (Table C-5). Available habitat area for adult resident trout at 205 cfs was significantly different than available habitat area at 345 cfs, at a level of alpha = 0.10 (Table D-5). Available habitat area for resident trout spawning increased as flows increased (Figure 3-6b), which was not the pattern of the other life stages graphs of habitat area versus discharge; however, relative habitat area remained very low at all flows (Table C-5). Available habitat for resident trout fry rearing appeared relatively stable as flows increased (Figure 3-6c). Suitable fry habitat was found exclusively along the margins of the lower Carmen Bypass Reach, where velocities and water depths were low enough to accommodate the habitat requirements of the guild. Relative habitat area for fry rearing was low (Table C-5). Available habitat areas for resident trout fry rearing at 160 and 345 cfs, 205 and 320 cfs, and 205 and 345 cfs, were significantly different from one another at a level of alpha = 0.10 (Table D-5). Relative habitat area for juvenile rearing ranged from high to very high. Available habitat areas at 160, 205, and 345 cfs were not significantly different from one another at a level of alpha = 0.10 (Table D-5). Juvenile and adult resident trout guilds were similar in habitat requirements, with juvenile resident trout rearing requiring less depth and therefore experiencing a slightly larger habitat area at each flow, compared with available habitat areas of adult cutthroat trout. 40

53 Table Estimated resident trout available habitat areas for all flows in the lower Carmen Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Adult Spawning Fry rearing Juvenile rearing 160 cfs 2,960 (± 531) 92 (± 34) 833 (± 153) 4,054 (± 642) 205 cfs 3,548 (± 363) 97 (± 31) 931 (± 140) 4,780 (± 809) 320 cfs NA 1 NA (± 116) NA cfs 2,797 (± 306) 223 (± 59) 555 (± 133) 4,031 (± 411) Estimated available habitat area in ft 2 (90% confidence interval) Flow Adult Spawning Fry rearing Juvenile rearing 160 cfs 31,861 (± 5,716) 990 (± 366) 8,966 (± 1,647) 43,637 (± 6,910) 205 cfs 38,190 (± 3,907) 1,044 (± 334) 10,021 (± 1,507) 51,451 (± 8,708) 320 cfs NA 1 NA 1 7,233 (± 1,249) NA cfs 30,107 (± 3,294) 2,400 (± 635) 5,974 (± 1,432) 43,389 (± 4,424) 1 Suitable habitat area for this life stage was not measured Smith Bypass Reach For resident trout in the Smith Bypass Reach, available habitat area was estimated for four life stages (adult, spawning, fry rearing, and juvenile rearing) at five flows (7, 20, 50, 85, and 120 cfs) (Table 3-17, Figures 3-7a d). As flows increased, available habitat area for resident trout adult and juvenile life stages were relatively stable, spawning habitat area increased, and fry habitat area decreased. At lower flows (7 and 20 cfs), suitable habitat for the adult resident trout generally extended across the channel, becoming concentrated along the channel margins at higher flows (50 to 120 cfs). Suitable water velocity appeared to be more restrictive than water depth and minimum area. Relative habitat area for adult resident trout was moderately and relatively stable over the flows measured (Table C-6). Adult resident trout available habitat was highest at 50 cfs (Figure 3-7a), although available habitat area estimates for adult resident trout at various flows were not significantly different at a level of alpha = 0.10 (Table D-6). Relative habitat area for resident trout spawning was very low (Table C-6). As flows increased from 7 to 120 cfs, suitable habitat was observed to increase; however, at all five flows, available habitat areas were not significantly different from one another, at a level of alpha = 0.10 (Table D-6). Fry habitat area was greatest at 7 cfs (Figure 3-7c). As flows increased from 7 to 120 cfs, available habitat area decreased, with water velocity generally restricting the amount of suitable habitat. Relative habitat area for resident trout fry rearing ranged from low to moderate in the Smith Bypass Reach (Table C-6). For resident trout fry rearing, available habitat area at 7 cfs was significantly different from available habitat areas at 50, 85, and 120 cfs; available habitat area at 20 cfs was significantly different from available habitat area at 85 and 120 cfs, at a level of alpha = 0.10 (Table D-6). Available habitat area for resident trout juveniles was greatest at 50 cfs, and was greater than the available habitat areas of the other three life stages (Figure 3-7d). Relative habitat area for resident trout fry rearing was moderate (Table C-6). Available habitat areas for juvenile resident trout at the five flows were not significantly different at a level of alpha = 0.10 (Table D-6). 41

54 Table Estimated resident trout available habitat areas for all flows in the Smith Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Adult Spawning 1 Fry rearing Juvenile rearing 7 cfs 4,083 (± 1,245) 38 (± 45) 3,397 (± 1,225) 7,000 (± 2,582) 20 cfs 3,995 (± 1,156) 62 (± 35) 2,753 (± 1,291) 5,650 (± 1,684) 50 cfs 5,324 (± 1,855) 99 (± 92) 1,737 (± 919) 7,587 (± 2,421) 85 cfs 4,606 (± 1,472) 112 (± 67) 1,244 (± 912) 6,641 (± 2,154) 120 cfs 4,570 (± 1,420) 131 (± 116) 1,123 (± 576) 6,091 (± 1,959) Estimated available habitat area in ft 2 (confidence interval) Flow Adult Spawning 1 Fry rearing Juvenile rearing 7 cfs 43,949 (± 13,401) 409 (± 484) 36,565 (± 13,186) 75,347 (± 27,792) 20 cfs 43,002 (± 12,443) 667 (± 377) 29,633 (± 13,896) 60,816 (± 18,126) 50 cfs 57,307 (± 19,967) 1,066 (± 990) 18,697 (± 9,892) 81,666 (± 26,059) 85 cfs 49,579 (± 15,844) 1,206 (± 721) 13,390 (± 9,817) 71,483 (± 23,185) 120 cfs 49,191 (± 15,285) 1,410 (± 1,249) (± 6,200) 65,563 (± 21,087) 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the variability in patch size Mountain whitefish Available habitat was assessed for two life stages of mountain whitefish (fry rearing and juvenile rearing). Mountain whitefish fry were included in the same life stage guild as other trout fry, and juveniles were included in the guild with other species juvenile life stages. During pilot surveys, suitable habitat areas for mountain whitefish adult and spawning life stages were found to be relatively high, and to increase with increasing flow based on 2D modeling (Addley et al. 2005). Therefore, the IFCT decided that suitable habitat areas for these two life stages would not be mapped Lower Carmen Bypass Reach Available habitat for mountain whitefish fry was assessed at four flows (160, 205, 320, and 345), and juvenile rearing habitat was assessed at three flows (160, 205, and 345). In the lower Carmen Bypass Reach, suitable habitat for mountain whitefish fry rearing was highest at 205 cfs (Table 3-18). Although habitat availability appears relatively stable over the range of flows measured (Figure 3-8a), available habitat areas for mountain whitefish fry rearing at 160 and 345 cfs, 205 and 320 cfs, and 205 and 345 cfs, were significantly different from one another at a level of alpha = 0.10 (Table D-7). Relative habitat area for mountain whitefish juvenile rearing was high (Table C-7), and highest at 205 cfs (Figure 3-8b). Rearing habitat for juvenile whitefish at 160, 205, and 345 cfs were not significantly different from one another at a level of alpha = 0.10 (Table D-7). 42

55 Table Estimated mountain whitefish available habitat areas for all flows in the lower Carmen Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Fry rearing Juvenile rearing 160 cfs 833 (±153) 4,054 (±642) 205 cfs 931 (±140) 4,780 (±809) 320 cfs 672 (±116) NA cfs 555 (±133) 4,031 (±411) Estimated available habitat area in ft 2 (90% confidence interval) Flow Fry rearing Juvenile rearing 160 cfs 8,966 (±1,647) 43,637 (±6,910) 205 cfs 10,021 (±1,507) 51,451 (±8,708) 320 cfs 7,233 (±1,249) NA cfs 5,974 (±1,432) 43,389 (±4,424) 1 Suitable habitat area for this life stage was not measured Smith Bypass Reach Fry and juvenile mountain whitefish habitat were estimated at five flows (7, 20, 50, 85, and 120 cfs). Mountain whitefish fry rearing habitat in the Smith Bypass Reach was moderately abundant (Table 3-19). Available fry habitat area was greatest at 7 cfs, and available fry rearing habitat area decreased as flows increased from 7 to 120 cfs (Figure 3-9a). For fry rearing, available habitat area at 7 cfs was significantly different from available habitat areas at 50, 85, and 120 cfs; available habitat area at 20 cfs was significantly different from available habitat area at 85 and 120 cfs, at a level of alpha = 0.10 (Table D-8). Juvenile mountain whitefish rearing habitat was greatest at 50 cfs, and was greater than the available habitat areas of the other three life stages (Figure 3-9b). Relative habitat area for mountain whitefish juvenile rearing ranged from high to very high (Table C-8). Available habitat areas for juvenile whitefish rearing at the five flows were not significantly different at a level of alpha = 0.10 (Table D-8). Table 3-19 Estimated mountain whitefish available habitat areas for all flows in the Smith Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Fry rearing Juvenile rearing 7 cfs 3,397 (± 1,225) 7,000 (± 2582) 20 cfs 2,753 (± 1,291) 5,650 (± 1,684) 50 cfs 1,737 (± 919) 7,587 (± 2,421) 85 cfs 1,244 (± 912) 6,641 (± 2,154) 120 cfs 1,123 (± 576) 6,091 (± 1,959) Estimated available habitat area in ft 2 (90% confidence interval) Flow Fry rearing Juvenile rearing 7 cfs 36,565 (± 13,186) 75,347 (± 27,792) 20 cfs 29,633 (± 13,896) 60,816 (± 18,126) 50 cfs 18,697 (± 9,892) 81,666 (± 26,059) 85 cfs 13,390 (± 9,817) 71,483 (± 23,185) 120 cfs (± 6,200) 65,563 (± 21,087) 43

56 3.3.5 Pacific lamprey Available habitat was assessed for two life stages of Pacific lamprey (spawning and juvenile rearing). Pacific lamprey spawning habitat was included in the guild with Chinook salmon spawning (Table A-3). Juvenile habitat was included in the guild with other species juvenile life stages with an additional criterion for the presence of silt and sand substrates Lower Carmen Bypass Reach In the lower Carmen Bypass reach, available spawning habitat for Pacific lamprey was assessed at four flows (160, 205, 320, and 345), and rearing habitat was assessed at three flows (160, 205, and 345) (Table C-9). Pacific lamprey spawning habitat was highest at 205 cfs (Figure 3-10). Available habitat area for spawning at 205 cfs was significantly different from available habitat areas for spawning at 160 and 345 cfs, at a level of alpha = 0.10 (Table D-9). No Pacific lamprey juvenile rearing habitat was identified due to the absence of fine sand and silt substrates in the reach (Table 3-20). Table Estimated Pacific lamprey available habitat areas for all flows in the lower Carmen Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Spawning Juvenile rearing 160 cfs 67 (± 26) cfs 144 (± 36) cfs 92 (± 40) NA cfs 58 (± 33) 0 Estimated available habitat area in ft 2 (90% confidence interval) Flow Spawning Juvenile rearing 160 cfs 721 (± 280) cfs 1,551 (± 388) cfs 990 (± 431) NA cfs 624 (± 355) 0 1 Suitable habitat area for this life stage was not measured Smith Bypass Reach For Pacific lamprey in the Smith Bypass Reach, available habitat area was estimated at five flows (7, 20, 50, 85, and 120 cfs) (Tables 3-21 and C-10; Figure 3-11). Pacific lamprey spawning habitat generally increased as flows increased. Available habitat area for spawning at 7 cfs was significantly different from available habitat area for spawning at 120 cfs, at a level of alpha = 0.10 (Table D-10). No Pacific lamprey juvenile rearing habitat was identified due to the absence of fine sand and silt substrates in the reach (Table 3-21). Table Estimated Pacific lamprey available habitat areas for all flows in the Smith Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Spawning 1 Juvenile rearing 7 cfs cfs 22 (± 46) 0 50 cfs 13 (± 26) 0 44

57 Estimated available habitat area in m 2 (90% confidence interval) Flow Spawning 1 Juvenile rearing 85 cfs 13 (± 26) cfs 82 (± 79) 0 Estimated available habitat area in ft 2 (90% confidence interval) Flow Spawning 1 Juvenile rearing 7 cfs cfs 237 (± 495) 0 50 cfs 140 (± 280) 0 85 cfs 140 (± 280) cfs 883 (± 850) 0 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the variability in patch size Western brook lamprey Available habitat was assessed for two life stages of western brook lamprey (spawning and juvenile rearing). Western brook lamprey spawning habitat was included in the guild with resident trout spawning. Juvenile habitat was included in the guild with other species juvenile life stages with an additional criterion for the presence of silt and sand substrates Lower Carmen Bypass Reach In the lower Carmen Bypass Reach, available habitat was assessed for western brook lamprey spawning and juvenile rearing life stages at three flows (160, 205, and 345) (Table C-11). Western brook lamprey spawning habitat increased as flow increased (Figure 3-12). Available habitat areas for western brook lamprey spawning at 160, 205, and 345 were not significantly different from one another at a level of alpha = 0.10 (Table D-11). No western brook lamprey juvenile rearing habitat was identified due to the absence of fine sand and silt substrates in the reach (Table 3-22). Table Estimated western brook lamprey available habitat areas for all flows in the lower Carmen Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Spawning Juvenile rearing 160 cfs 92 (± 34) cfs 97 (± 31) cfs NA 1 NA cfs 223 (± 59) 0 Estimated available habitat area in ft 2 (90% confidence interval) Flow Spawning Juvenile rearing 160 cfs 990 (± 366) cfs 1,044 (± 336) cfs NA 1 NA cfs 2,400 (± 635) 0 1 Suitable habitat area for this life stage was not measured. 45

58 Smith Bypass Reach In the Smith Bypass Reach, available spawning and juvenile rearing habitat for western brook lamprey were assessed at five flows (7, 20, 50, 85, and 120) (Table C-12). Available habitat area for spawning at 7 cfs was significantly different from available habitat area for spawning at 120 cfs, at a level of alpha = 0.10 (Table D-12). Western brook lamprey spawning habitat increased as flow increased (Figure 3-13). Available spawning habitat area for western brook lamprey was relatively low (Table 3-23). No western brook lamprey juvenile rearing habitat was identified due to the absence of fine sand and silt substrates in the reach. Table Estimated western brook lamprey available habitat areas for all flows in the Smith Bypass Reach. Estimated available habitat area in m 2 (90% confidence interval) Flow Spawning 1 Juvenile rearing 7 cfs 38 (± 45) 0 20 cfs 62 (± 35) 0 50 cfs 99 (± 92) 0 85 cfs 112 (± 67) cfs 131 (± 116) 0 Estimated available habitat area in ft 2 (90% confidence interval) Flow Spawning 1 Juvenile rearing 7 cfs 409(± 484) 0 20 cfs 667(± 377) 0 50 cfs 1,066(± 990) 0 85 cfs 1,206(± 721) cfs 1,410(± 1,249) 0 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the variability in patch size Detritus The detritus cover type was considered to provide potentially greater habitat value for bull trout fry than other cover types and was mapped separately using three mutually exclusive detritus cover types (detritus cover only, detritus with other cover, and cover with no detritus) (Figures 3-14a b). In the lower Carmen Bypass Reach, the total area of detritus cover only plus detritus with other cover is generally greater than area of cover with no detritus. The exception occurs at 320 cfs, when the sum is less than the area of cover with no detritus. Areas of detritus cover only and detritus with other cover had similar trends from 205 cfs to 345 cfs (Figure 3-14a). Areas of detritus with other cover and of cover with no detritus exhibited opposite trends. Trends noted for detritus results are possibly influenced by the progression and timing of mapping flows (as noted in Table 3-10), since detritus tends to be composed of small, mobile particles that can be redistributed during high flows. Thus, measured amounts of detritus could be different for surveys having an alternate sequence of studied flows. In the Smith Bypass Reach, the area of detritus cover only and the area of detritus with other cover generally increased as flows increased (Figure 3-14b). Cover with no detritus was greatest at 7 cfs and decreased over the range of flows mapped. The increase in detritus cover with increase in flow is likely the result of higher flows inundating areas with accumulated organic matter, rather than higher flows redistributing detritus elements. No consistent trends were 46

59 evident between reaches over the range of flows mapped. Cover associated with detritus did not decrease as flows increased Large woody debris The influence of large woody debris (LWD) on habitat availability was assumed to increase habitat similarly at all flows. To evaluate this assumption, the habitat area to flow relationship was compared under two conditions: (1) in habitat units with relatively high existing LWD levels compared with those with relatively low levels of existing LWD (high/low test), and (2) in locations in close proximity to (and likely influenced by) existing LWD accumulations, compared with locations away from, or not influenced by, existing LWD accumulations (proximity test). For the first comparison, five of the 20 habitat units mapped in the lower Carmen Bypass Reach were designated as having relatively high LWD loading, based on area of LWD delineated (at 345 cfs) during habitat mapping (Table 3-24). For the second comparison, six of the 20 habitat units in the lower Carmen Bypass Reach were designated as having LWD accumulations (Table 3-24). Results from these evaluations are described below. Table Habitat area per site and LWD loading category in the lower Carmen Bypass Reach. Category Low wood loading Low wood loading, LWD accumulation High wood loading, LWD accumulation Habitat unit Area (site) m 2 ft 2 2A B B A A B D B D A C A A B A D Comparison of habitat units with relatively high to relatively low wood loading The amount of habitat area (per unit length) in habitat units with high wood loading (blue distributions) and low wood loading (red distributions) were plotted for five guilds (cutthroat adult, bull trout spawning, adult resident trout spawning, trout fry rearing, and salmonid juvenile rearing), over the range of flows mapped (Figures 3-15a e). For habitat units with high and low 47

60 wood loading, a comparison of flow-habitat relationships indicated no consistent trend (Figures 3-15 a e). T-tests (alpha = 0.10) were conducted to determine whether habitat areas were significantly different between flows, in order to examine how the change in habitat area with flow differs between the high and low wood loading units. As expected, suitable habitat area at any given discharge was generally greater in habitat units having high wood loading compared with habitat units having low wood loading (i.e., the blue shaded areas are above the red shaded areas), indicating the relative benefit of wood (Figures 3-15a e). In habitat units with high wood loading, habitat area for the cutthroat trout adult guild appeared to increase from 160 to 205 cfs, and did not change from 205 to 345 cfs (Figure 3-15a); high wood loading habitat areas were not significantly different between flows at a level of alpha = 0.10 (Table D-13). In habitat units with low wood loading, cutthroat trout adult habitat area appeared to increase from 160 to 205 cfs, and decrease from 205 and 345 cfs (Figure 3-15a); at 205 cfs, low wood loading areas for the cutthroat trout adult guild were significantly different from low wood loading areas at 345 cfs, at a level of alpha = 0.10 (Table D-14). For the adult resident trout spawning guild, in habitat units with high wood loading, habitat area decreased from 160 to 205 cfs, but increased from 205 to 345 cfs (Figure 3-15b); high wood loading habitat areas were not significantly different between flows at a level of alpha = 0.10 (Table D-13). In habitat units with low wood loading, adult resident trout spawning guild habitat area increased from 160 to 205 cfs, and from 205 to 345 cfs (Figure 3-15b); at 160 and 205 cfs, low wood loading areas for the adult resident trout spawning guild were significantly different from low wood loading habitat areas at 345 cfs, at a level of alpha = 0.10 (Table D-14). For the bull trout spawning guild, in habitat units with high wood loading, habitat area increased substantially from 160 to 205 cfs, and decreased substantially from 205 and 320, and from 320 to 345 cfs (Figure 3-15c); high wood loading habitat area at 205 cfs was significantly different from habitat areas at 320 and 345 cfs, and habitat area at 320 cfs was significantly different from habitat area at 345 cfs, at a level of alpha = 0.10 (Table D-13). In habitat units with low wood loading, bull trout spawning habitat area increased from 160 to 205 cfs, changed little from 205 to 320 cfs, and decreased from 320 to 345 cfs (Figure 3-15c); low wood loading habitat areas for the bull trout spawning guild were not significantly different between flows, at a level of alpha = 0.10 (Table D-14). For the trout and char fry rearing guild, little change in habitat area was apparent, in units with high and low wood loading, between flows (Figure 3-15d); high wood loading habitat areas were not significantly different between flows, at a level of alpha = 0.10 (Table D-13). In habitat units with low wood loading, trout and char fry rearing areas at 160, 205, and 320 cfs were significantly different from habitat area at 345 cfs; trout and fry rearing area at 205 cfs was significantly different from habitat area at 320 cfs, at a level of alpha = 0.10 (Table D-14, Figure 3-15d). For the juvenile salmonid rearing guild, in habitat units with high wood loading, habitat area increased from 160 to 205 cfs, and from 205 to 345 cfs (Figure 3-15e). For the juvenile salmonid rearing guild, in habitat units with low wood loading, a habitat area increase is suggested from 160 to 205 cfs, and a decrease is suggested from 205 to 345 cfs. In units with both high and low wood loading, juvenile salmonid rearing guild habitat areas were not significantly different between flows, at a level of alpha = 0.10 (Tables D-13 and D-14). By graphing the habitat area of the high wood loading units on the same axes as the habitat areas resulting from the full criteria mapping effort (Figure 3-16a e), the potential effects of conducting 48

61 habitat enhancements using LWD can be evaluated. Results from this comparison are similar to the results from the comparison of habitat units with relatively high to relatively low wood loading, indicating that the lower Carmen Bypass Reach had relatively low wood loading at that time Comparison of suitable habitat area in close proximity, and not in close proximity, to wood accumulations A second test was conducted to assess whether the flow-habitat relationship is affected by wood. The amount of suitable habitat area for locations in close proximity to wood accumulations (i.e., inside buffers), compared with locations not in close proximity, or away from wood accumulations (i.e., outside buffers), was evaluated using a 3-m (10-ft) buffer around the wood accumulations that were mapped at 345 cfs. Suitable habitat area inside and outside of these buffers was calculated for the five guilds, using GIS over the range of flows mapped (Figures 3-17a e). T-tests (alpha = 0.10) were conducted to determine whether suitable habitat areas were significantly different between flows in order to examine how the change in habitat area with flow differs between areas in close proximity, and not in close proximity, to wood accumulations. Suitable habitat area was generally greater in close proximity to wood accumulations than farther away from wood accumulations, indicating the relative benefit of wood. For habitat in close proximity, and not in close proximity, to wood accumulations, flow-habitat relationships indicated no consistent trend (Figures 3-17 a e). For the cutthroat trout adult guild, habitat area in close proximity to wood accumulations (i.e., areas inside buffers) increased as flows increased, but habitat areas away from wood accumulations (i.e., areas outside buffers) did not (Figure 3-17a). Cutthroat trout adult habitat areas outside of buffers increased from 160 to 205 cfs, but then decreased from 205 to 345 cfs. Although their apparent relationships to flow are different, for the cutthroat trout adult guild, habitat areas inside of the buffers and that outside of the buffers were not significantly different between flows, at a level of alpha = 0.10 (Tables D-15 and D-16). For the adult resident trout spawning guild, habitat areas in close proximity to wood accumulations (i.e., areas inside buffers) and habitat areas away from wood accumulations (areas outside buffers) increased as flows increased (Figure 3-17b). Adult resident trout spawning habitat areas in close proximity to wood accumulations (inside buffers) and those areas outside of buffers, were not significantly different between flows, at a level of alpha = 0.10 (Tables D-15 and D-16). For the bull trout spawning guild, habitat areas in close proximity to wood accumulations (i.e., areas inside buffers) did not change from 160 to 205 cfs, and from 205 to 320 cfs, but then decreased to zero from 320 to 345 cfs (Figure 3-17c; note the line at 345 cfs and 0.0 habitat area, indicating no habitat area at the flow, with no confidence interval computed). Habitat areas away from wood accumulations (i.e., areas outside of buffers) increased from 160 to 205 cfs, but then decreased from 205 to 320 cfs, and from 320 to 345 cfs. Bull trout spawning habitat area in close proximity to wood accumulations (inside buffers) at 205 cfs was significantly different than habitat area at 345 cfs, at a level of alpha = 0.10 (Table D-15). Bull trout spawning habitat area outside of buffers at 320 cfs was significantly different from habitat area at 345 cfs, at a level of alpha = 0.10 (Table D-16). For the trout and char fry rearing guild, habitat areas in close proximity to wood accumulations (i.e., inside buffers) and habitat areas away from wood accumulations (i.e., outside buffers) changed little between flows (Figure 3-17d). Trout and char fry rearing habitat areas in close 49

62 proximity to wood accumulations (inside buffers) were not significantly different between flows, at a level of alpha = 0.10 (Table D-15). Trout and char fry rearing habitat area away from wood accumulations (outside buffers) at 205 cfs was significantly different from habitat area at 345 cfs, at a level of alpha = 0.10 (Table D-16). For juvenile salmonid rearing guild, habitat areas in close proximity to wood accumulations (inside buffers) increased as flows increased (Figure 3-17e). Habitat areas away from wood accumulations (outside buffers) did not change from 160 to 205 cfs, but then decreased from 205 to 345 cfs. Juvenile salmonid rearing habitat area in close proximity to wood accumulations (inside buffers) at 205 cfs was significantly different than habitat area at 345 cfs, at a level of alpha = 0.10 (Table D-15). Juvenile salmonid rearing habitat areas away from wood accumulations (outside buffers) were not significantly different between flows, at a level of alpha = 0.10 (Table D-16). The evaluation of habitat in close proximity, and not in close proximity, to wood accumulations was conducted to evaluate the effects of wood on habitat for the flows measured, and was expected to illustrate greater differences than the test comparing habitat units with relatively high to relatively low wood loading, because of the smaller scale of the areas being compared (the scale of an individual LWD accumulation vs. the scale of a habitat unit). Note that it may be unrealistic to assume that enhancements of this scale (and effect) would be feasible or desired. 3.4 Habitat Availability in Unregulated Reaches Habitat mapping results in the unregulated reaches showed relationships similar to those in the regulated reaches in the quantity of habitat mapped for the guilds. The salmonid juvenile rearing guild was mapped extensively in unregulated reaches due to the wide range of water velocities and water depth criteria for this guild. The cutthroat trout adult guild had similar depth and velocity criteria to the salmonid juvenile guild, but the criteria for deeper water and a larger polygon size often restricted the areas suitable for cutthroat trout adults compared with salmonid juvenile. No bull trout adult or Chinook salmon habitat was found, and the scarcity appeared to be limited by water depths, which were less than 1.7 m (5.5 ft). Habitat suitability was mapped independent of water temperature. Bull trout and Chinook salmon spawning guilds had similar habitat criteria, and similar habitat areas were found. In the unregulated reaches studied, suitable spawning substrate was more restrictive than water depth or water velocity in mapping suitable areas for spawning guilds, and habitat areas for all spawning guilds were relatively small. Sweetwater Creek had the largest spawning habitat area mapped for all three spawning guilds within the unregulated reaches. Suitable habitat for fry rearing guilds was mapped primarily on stream margins where water velocities were lowest. For the trout and char fry rearing guild, suitable habitat was located almost exclusively on stream margins. Suitable habitat for Chinook salmon fry rearing was often in the same locations as trout and char fry rearing habitat, but could extend further into the channel and into areas of higher flows. Chinook salmon suitable habitat areas were extrapolated to the reach of the Smith River upstream of Smith Reservoir to the confluence with Browder Creek, based on a consensus of IFCT members professional judgments. Suitable habitat areas for other species and life stages were extrapolated throughout the entire reach, and were not restricted to reaches downstream of the confluence with Browder Creek. 50

63 The unregulated reach habitat mapping results include areas in Sweetwater Creek, Kink Creek, Smith River upstream of Smith Reservoir, and Browder Creek (Figures 3-18 a p), which were mapped in May 2005 (Table 3-25). Habitat maps for the unregulated reaches at each habitat unit were generated (Appendix G). Table Summary of flows during habitat availability assessment in unregulated reaches in Location Mapping Estimated discharge dates (cfs) Sweetwater Creek May 44 cfs on 6 May Kink Creek May 6 cfs on 6 May Smith River upstream of Daily average discharge for all 12, 14, and Smith Reservoir and dates combined was 113 cfs, May Browder Creek with a range of cfs Flows in Sweetwater Creek are highly stable throughout the year, due to the strong groundwater influence of the High Cascades geology. Preliminary results from a stage gaging station on this stream (Jefferson et al. 2006, in preparation), as well as macroinvertebrate sampling results from this study (Section 3.8), reflect the stable nature of this system. Kink Creek is an ungaged tributary of the lower Carmen Bypass Reach. In addition to the 6 cfs discharge measured on 6 May, only one other discharge measurement (2 cfs in 30 October 2003) has been recorded for this creek. Daily average flows for mapping in the Smith River upstream of Smith Reservoir are monitored at the USGS gage # , and ranged from 77 to 145 cfs during habitat mapping efforts. These flows are consistent with flows that would be encountered in the months of November through June. In the dry months of July October, average monthly flows decrease to 7 22 cfs Bull trout Sweetwater Creek No suitable adult bull trout habitat was identified in Sweetwater Creek (Table 3-26). Adult bull trout available habitat area was limited by the 1.7-m (5.5-ft) minimum water depth criteria. The relative area of bull trout spawning habitat was very low (Table C-13), with about 162 m 2 (1,744 ft 2 ) of available habitat in the reach (Table 3-26). Much of the gravel present in Sweetwater Creek was smaller than the size criterion for suitable bull trout spawning substrate. Relative area of bull trout early fry rearing habitat area was also found to be very low (Table C-13), with 281 m 2 (3,025 ft 2 ) of habitat estimated (Table 3-26). Relative area of bull trout late fry rearing habitat was low (Table C-13), with 881 m 2 (9,483 ft 2 ) of estimated available habitat area (Table 3-26). Relative area of bull trout juvenile rearing habitat was high (Table C-13), with a total of 2,637 m 2 (28,384 ft 2 ) of habitat area estimated in the reach (Table 3-26). All assessments of bull trout habitat were made independent of a temperature criterion. 51

64 Table Estimated bull trout available habitat area in Sweetwater Creek. Life stage Estimated available habitat area in m 2 (90% confidence interval) Estimated available habitat area in ft 2 (90% confidence interval) Adult 0 0 Spawning 162 (± 86) 1,744 (± 926) Early fry rearing 281 (± 67) 3,025 (± 721) Late fry rearing 881 (± 262) 9,483 (± 2,820) Juvenile rearing 2,637 (± 523) 28,384 (± 5,630) Kink Creek No suitable adult or spawning bull trout habitat area was identified in Kink Creek (Table 3-27). Habitat area was limited by the relatively shallow water depths and absence of suitable gravel patches. Access to Kink Creek during the bull trout spawning period may be restricted due to low discharge and subsurface flow at the confluence. Relative area of bull trout early fry rearing habitat was very low (Table C-14), with 29 m 2 (312 ft 2 ) of available habitat area estimated (Table 3-27). Relative area of late fry rearing habitat area was moderate (Table C-14), with 88 m 2 (947 ft 2 ) of available habitat area estimated (Table 3-27). Bull trout juvenile rearing habitat was the most abundant habitat type in Kink Creek, with 135 m 2 (1,453 ft 2 ) of habitat area estimated in the reach (Table 3-27). Relative area of juvenile bull trout habitat was high (Table C-14). Under low flow conditions, juvenile rearing habitat would likely be lower than estimated here. In the late summer and fall, flow in Kink Creek is intermittent or completely dry. All assessments of bull trout habitat were made independent of a temperature criterion. Table Estimated bull trout available habitat area in Kink Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 0 0 Spawning 0 0 Early fry rearing 29 (± 8) 312 (± 86) Late fry rearing 88 (± 34) 947 (± 366) Juvenile rearing 135 (± 31) 1,453 (± 334) Smith River upstream of Smith Reservoir and Browder Creek No suitable adult bull trout habitat was identified in Smith River upstream of Smith Reservoir or in Browder Creek (Table 3-28). Adult bull trout habitat area was limited by the 1.7-m (5.5-ft) minimum water depth criterion. Relative area of bull trout spawning habitat area was very low (Table C-15), with a total of 45 m 2 (484 ft 2 ) of habitat area estimated (Table 3-28). For bull trout early fry rearing, the estimated habitat area was 583 m 2 (6,275 ft 2 ) (Table 3-28), and relative habitat area was very low (Table C-15). For bull trout late fry rearing estimated habitat area was 1,282 m 2 (13,799 ft 2 ), and relative habitat area was moderate. Relative area of juvenile rearing habitat for bull trout was low, with a total of 3,137 m 2 (33,766 ft 2 ) of habitat estimated in the reach (Table 3-28). Juvenile rearing habitat would likely be lower under low flow conditions. All assessments of bull trout habitat were made independent of the ODEQ (2002) temperature criterion; however, high water temperatures upstream of Smith reservoir during late summer and fall are expected to preclude the suitability of this habitat for late fry rearing, juvenile rearing, and 52

65 adult life stages. Temperature constraints will be integrated into the population dynamics model where appropriate. Table Estimated bull trout available habitat area in Smith River above Smith Reservoir and Browder Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 0 0 Spawning 1 45 (± 72) 484 (± 775) Early fry rearing 583 (± 271) 6,275 (± 2,917) Late fry rearing 1,282 (± 428) 2 13,799 (± 4,607) 2 Juvenile rearing 3,137 (± 741) 2 33,766 (± 7,976) 2 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the natural variability in patch size. 2 Water temperature was not considered in the estimate of available habitat and will preclude suitability of this habitat. Under current conditions water temperature during late summer limits suitability of this habitat Chinook salmon Sweetwater Creek In Sweetwater Creek, a total of approximately 124 m 2 (1,335 ft 2 ) of Chinook salmon spawning habitat area was estimated (Table 3-29). This is slightly less than the spawning habitat area estimated for bull trout (162 m 2 [1,744 ft 2 ]). Much of the gravel present in Sweetwater Creek was smaller than the size criterion for Chinook salmon suitable spawning substrate. The Chinook salmon fry rearing habitat area estimate is 881 m 2 (9,483 ft 2 ) (Table 3-29). Relative area of Chinook salmon juvenile rearing habitat was high (Table C-16), with a total of 2,637 m 2 (28,384 ft 2 ) of habitat area estimated in the reach (Table 3-29). No Chinook salmon adult habitat was identified (Table 3-29). Although habitat availability for Chinook salmon was assessed in Sweetwater Creek, Chinook salmon have not been documented in this tributary. Table Estimated Chinook salmon available habitat area in Sweetwater Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 0 0 Spawning 124 (± 71) 1,335 (± 764) Fry rearing 881 (± 262) 9,483 (± 2,820) Juvenile rearing 2,637 (± 523) 28,384 (± 5,630) Kink Creek No Chinook salmon spawning habitat area was found in Kink Creek (Table 3-30), due to the absence of suitable gravel patches that were large enough to fulfill the minimum polygon size criteria. Adult habitat area was also unavailable (Table 3-30). Access to Kink Creek during the Chinook salmon spawning period (from the beginning of September through early October) may be restricted due to lack of surface flow at the confluence with the McKenzie River. Relative area of Chinook salmon fry rearing habitat area was low (Table C-17), with a total of 88 m 2 (947 53

66 ft 2 ) of habitat present (Table 3-30). Chinook salmon juvenile rearing habitat was the most abundant type of habitat, with 135 m 2 (1,453 ft 2 ) of available habitat area in Kink Creek (Table 3-30). Relative area of juvenile rearing habitat was low (Table C-17). In the late summer and fall, flow in Kink Creek is intermittent or completely dry. Table Estimated Chinook salmon available habitat area in Kink Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 0 0 Spawning 0 0 Fry rearing 88 (± 34) 947 (± 366) Juvenile rearing 135 (± 31) 1,453 (± 334) Smith River Upstream of Smith Reservoir and Browder Creek For the purposes of this study, Chinook salmon habitat upstream of Smith Reservoir was considered to extend upstream to the confluence with Browder Creek. The upper Smith River (upstream of the confluence with Browder Creek) and Browder Creek are relatively small channels (3 8 m width) with relatively steep gradient (5% average) for Chinook salmon. The relative area of Chinook salmon spawning habitat was very low (Table C-18), with an estimate of 38 m 2 (409 ft 2 ) for the reach (Table 3-31). Relative area of Chinook salmon fry rearing habitat was low (Table C-18), with 613 m 2 (2,011 ft 2 ) of habitat estimated (Table 3-31). Relative area of juvenile rearing habitat was moderate (Table C-18), with 1,583 m 2 (5,194 ft 2 ) of habitat area estimated in the reach (Table 3-31). Juvenile rearing habitat would likely be lower that reported here under low-flow conditions. Table Estimated Chinook salmon available habitat area in the Smith River above Smith Reservoir and Browder Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 0 0 Spawning 1 38 (± 176) 409 (± 1,894) Fry rearing 1,282 (± 428) 2 13,799 (± 4,607) 2 Juvenile rearing 3,137 (± 741) 33,766 (± 7,976) 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the natural variability in patch size. 2 Water temperature was not considered in the estimate of available habitat and will preclude suitability of this habitat. Under current conditions water temperature during late summer limits suitability of this habitat Resident trout Resident trout include cutthroat trout, rainbow trout, and brook trout. All life stages of these species were included into the same guilds because they have similar habitat criteria Sweetwater Creek In Sweetwater Creek, relative area of adult resident trout habitat was low, with 596 m 2 (6,415 ft 2 ) estimated in the reach. Habitat areas suitable for adult resident trout were highly variable 54

67 between habitat units, which resulted in a wide confidence interval (±379 m 2, ±4,080 ft 2 ) for the estimate (Table 3-32). An area of 218 m 2 (2,347 ft 2 ) of resident trout spawning habitat was estimated in the reach, which was slightly greater than for bull trout or Chinook salmon, which is likely partly due to the smaller substrate particle size criterion for resident trout spawning habitat. For resident trout fry rearing, relative habitat area was very low (Table C-19), with 281 m 2 (3,025 ft 2 ) of habitat estimated in the reach (Table 3-32). Relative area of resident trout juvenile rearing habitat was high (Table C-19), with 2,637 m 2 (28,384 ft 2 ) estimated in the reach (Table 3-32). Table Estimated resident trout available habitat area in Sweetwater Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 596 (± 379) 6,415 (± 4,080) Spawning 218 (± 69) 2,347 (± 743) Fry rearing 281 (± 67) 3,025 (± 721) Juvenile rearing 2,637 (± 523) 28,384 (± 5,630) Kink Creek Relative area of adult resident trout available habitat was low in Kink Creek (Table C-20), with 56 m 2 (603 ft 2 ) (Table 3-33). No resident trout spawning habitat was found at the survey sites in the reach. Resident fry rearing habitat area was very low (Table C-20), with 29 m 2 (312 ft 2 ) (Table 3-33). Resident trout juvenile rearing habitat was relatively low (Table C-20), although it was the most abundant habitat type in Kink Creek with 135 m 2 (1,453 ft 2 ) estimated for the reach (Table 3-33). Kink Creek may have intermittent flow or complete subsurface flow in the late summer and fall. Table Estimated resident trout available habitat area in Kink Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 56 (± 30) 603 (± 323) Spawning 0 0 Fry rearing 29 (± 8) 312 (± 86) Juvenile rearing 135 (± 31) 1,453 (± 334) Smith River upstream of Smith Reservoir and Browder Creek Relative area of adult resident trout habitat was very low in the Smith River upstream of Smith Reservoir and in Browder Creek (Table C-21), with 1,803 m 2 (19,407 ft 2 ) of habitat estimated for the reach (Table 3-34). Relative area of resident trout spawning habitat was very low (Table C- 21), with habitat area slightly less than the area for Chinook salmon spawning. Relative area of resident trout fry and juvenile rearing habitat was very low and low, respectively (Table C-21). A total area of 583 m 2 (6,275 ft 2 ) of fry habitat and 3,137 m 2 (33,766 ft 2 ) of juvenile habitat was estimated for the reach (Table 3-34). 55

68 Table Estimated resident trout available habitat area in the Smith River above Smith Reservoir and in Browder Creek. Life stage Estimated available habitat area Estimated available habitat area in m 2 (90% confidence interval) in ft 2 (90% confidence interval) Adult 1,803 (± 388) 19,407 (± 4,186) Spawning 75 (± 31) 807 (± 334) Fry rearing 583 (± 271) 6,275 (± 2,917) Juvenile rearing 3,137 (± 741) 33,766 (± 7,976) Mountain whitefish Adult habitat and spawning habitat for whitefish were not mapped because habitat areas for those life stages were shown to increase with increasing flow based on the 2D modeling; therefore, mapping for those life stages was determined to be unnecessary. For mountain whitefish, the fry rearing and juvenile rearing life stages were mapped and included in the same guilds as resident trout. The three unregulated reaches in which mountain whitefish were mapped are Sweetwater Creek, Kink Creek, and the Smith River upstream of Smith Reservoir and Browder Creek (Table 3-35). Mountain whitefish have not been observed in Sweetwater or Kink creeks. Relative area of mountain whitefish fry habitat was very low in all reaches (Table C-22). Relative area of juvenile mountain whitefish rearing habitat in Sweetwater Creek was high with 2,637 m 2 (28,384 ft 2 ) of habitat estimated (Table 3-35). Relative area of juvenile mountain whitefish rearing habitat in Kink Creek and the Smith River upstream of Smith Reservoir was low (Table C-22). Table Estimated mountain whitefish available habitat area in unregulated reaches. Estimated available habitat area in m 2 (90% confidence interval) Reach Fry rearing Juvenile rearing Sweetwater Creek 281 (± 67) 2,637 (± 523) Kink Creek 29 (± 8) 135 (± 31) Smith River Upstream of Smith Reservoir and Browder Creek 583 (± 271) 3,137 (± 741) Estimated available habitat area in ft 2 (90% confidence interval) Reach Fry rearing Juvenile rearing Sweetwater Creek 3,025 (± 721) 28,384 (± 5,630) Kink Creek 312 (± 86) 1,453 (± 334) Smith River Upstream of Smith Reservoir and Browder Creek 6,275 (± 2,917) 33,766 (± 7,976) Pacific lamprey The three unregulated reaches in which Pacific lamprey habitat were mapped are Sweetwater Creek, Kink Creek, and the Smith River upstream of Smith Reservoir and Browder Creek (Table 3-36). Pacific lamprey spawning habitat was included in the Chinook salmon spawning guild, and Pacific lamprey juvenile habitat was included in the other species juvenile life stage guild with an additional criterion for the presence of silt and sand substrates. 56

69 Table Estimated Pacific lamprey available habitat area in unregulated reaches. Estimated available habitat area in m 2 (90% confidence interval) Reach Spawning 1 Juvenile rearing Sweetwater Creek 124 (± 71) 1,796 (± 355) Kink Creek 0 0 Smith River Upstream of Smith Reservoir and Browder Creek 38 (± 176) 0 Estimated available habitat area in ft 2 (90% confidence interval) Reach Spawning 1 Juvenile rearing Sweetwater Creek 1,335 (± 764) 19,332 (±3,821) Kink Creek 0 0 Smith River Upstream of Smith Reservoir and Browder Creek 409 (± 1,894) 0 1 The relatively large confidence interval for spawning habitat is a result of the patchiness of suitable substrate and the variability in patch size. In Sweetwater Creek, relative area of Pacific lamprey spawning habitat was very low (Table C- 23), and juvenile rearing habitat was moderate (Table C-23), with habitat area estimates of 124 m 2 (1,335 ft 2 ) and 1,796 m 2 (19,332 ft 2 ), respectively (Table 3-36). In Kink Creek, no spawning or juvenile rearing habitat area for Pacific lamprey was found (Table 3-36). In the Smith River upstream of Smith Reservoir, relative area of Pacific lamprey spawning habitat was very low, with habitat reach estimates of 38 m 2.(409 ft 2 ). No juvenile rearing habitat for Pacific lamprey was found upstream of Smith Reservoir (Table 3-36) Western brook lamprey Western brook lamprey spawning and juvenile rearing habitats were included in the same guilds that represented similar life stages for resident trout, although juvenile rearing habitat included an additional criterion for the presence of fine sand and silt substrates. Relative area of western brook lamprey spawning habitat in Sweetwater Creek was very low (Table C-24), and juvenile rearing habitat was moderate (Table C-24). In Kink Creek, no spawning or rearing habitat was found for western brook lamprey (Table 3-37). In the Smith River upstream of Smith Reservoir, the relative area of western brook lamprey spawning habitat was very low (Table C-24), and no juvenile habitat was identified (Table 3-37). Table Estimated western brook lamprey available habitat area in unregulated reaches. Estimated available habitat area in m 2 (90% confidence interval) Reach Spawning Juvenile rearing Sweetwater Creek 218 (± 69) 1,796 (± 355) Kink Creek 0 0 Smith River Upstream of Smith Reservoir and Browder Creek Estimated available habitat area in ft 2 (90% confidence interval) Reach Spawning Juvenile rearing Sweetwater Creek 2,347 (± 743) 19,332 (± 3,821) Kink Creek 0 0 Smith River Upstream of Smith Reservoir and Browder Creek 1, Confidence intervals are not reported since extrapolations were extended beyond the sampling universe. 57

70 3.5 Habitat Availability in the Upper Carmen Bypass Reach In the upper Carmen Bypass Reach, aquatic habitat was assessed at a range of flow releases by documenting habitat conditions with photographs and video taken at specified photographic locations (photo points), measuring habitat characteristics in the field, and identifying the downstream extent of surface flow at the various releases. Carmen Diversion Dam releases of 0, 10, 50, 160, and 250 cfs were evaluated between 28 April 2005 and 13 May Because of the time lag between flow releases at Carmen Diversion Reservoir and flow levels in the Carmen Bypass Reach, high flows were released for several days so that flows in the bypass reach could reach equilibrium, as measured in the lower bypass reach. Flows were then stepped down to the discharges targeted for this assessment of the upper bypass reach (Figure 3-19). The dates when sampling occurred, the sizes of the flow releases, and the downstream extents of surface flows are summarized (Table 3-38); for each flow, photographs and video documented conditions at each photo/video point during the assessment (Appendices E and F). Additional information on the upper Carmen Bypass Reach hydrology is described in the Hydrologic Regimes technical report (Stillwater Sciences 2006b). Table Summary of target and measured discharges during available habitat area assessment in the upper Carmen Bypass Reach in Target discharge Flow release 1 (cfs) (cfs) Mapping dates April May May May May 1 Flow release is estimated from spill at Carmen Diversion Dam. Spill value given is average daily spill value for the survey date(s). The downstream extents of flows for each spill are summarized (Table 3-39). In October 2003, 330 cfs was released from Carmen Diversion Dam during a maintenance spill (Stillwater Sciences 2004b). Conditions observed during this spill event were considered informative for this assessment and are included; however, flow release observations noted for this event are given after a period of over two weeks of continuous spill, as compared with the much shorter duration of spill for the other sets of observations (Figure 2-2 and Table 3-39). Table Flow releases at Carmen Diversion Dam for conducting habitat mapping in the lower Carmen Bypass Reach. Date Flow release (cfs) Extent of surface flow downstream from Carmen Diversion Dam Estimated surface area downstream from Carmen Diversion Dam m ft m 2 ft 2 28 April , May ,205 6,808 73, May ,575 5,167 16, , May ,988 6,522 27, ,765 4 May ,795 9,170 49, , October ,409 11,184 56, , Surface area was estimated by adding area for the reach between the downstream extent of flow at 250 and 330 cfs, to the area estimated at 250 cfs. 58

71 3.5.1 No flow release Under no flow release conditions, a pool is located at the base of Carmen Diversion Dam, sourced from groundwater seepage and/or interception of the water table near the base of the dam (photo point 1). This pool extends from the base of the dam to 77 m (253 ft) downstream of the dam (Figures 3-20 and 3-21). Electrofishing surveys indicated that fish are able to survive in this pool throughout the year (Stillwater Sciences 2006f). No surface flow was observed at photo points 2 through 9 when no flow was released cfs flow release Under a 10 cfs flow release, the downstream extent of surface flow was observed 977 m (3,205 ft) downstream of the dam, and 320 m (1,050 ft) downstream of photo point 2 (Figures 3-20 and 3-21). At photo point 1, water depth in the pool increased by approximately 0.3 m (1 ft) from the 0 cfs flow release. Water generally remained still, with no discernable velocity. Downstream of photo point 1, vegetation growing in the channel became inundated. Channel conditions upstream of photo point 2 were generally open and grassy, with little woody vegetation in the channel. Wetted channel width at photo point 2 was approximately 48 m (157 ft). Water depth at photo point 2 was greater than 1 m (3 ft), although water depth was not measured because the channel was too deep to wade. Some partially submerged LWD in the vicinity of photo point 2 could have provided cover cfs flow release Under a 50 cfs flow release, the downstream extent of surface flow was 1,575 meters (5,167 ft) from Carmen Diversion Dam, which is approximately 250 m (820 ft) upstream of the first footbridge (photo point 3) (Figures 3-20 and 3-21). At 50 cfs, the pool in the vicinity of photo point 1 expanded and water depth increased by about 0.3 m (1 ft) relative to the 10 cfs flow release, and water velocity remained relatively still. Pool depth was not measured because the channel remained too deep to wade. At photo point 2, wetted channel width was approximately 50 m (164 ft). At 50 cfs, the leading edge was dammed by a large accumulation of woody debris that ponds water upstream. There was no discernable water velocity at the leading edge of flow cfs flow release Under a 160 cfs flow release, the downstream extent of surface flow was 1,988 m (6,522 ft) from Carmen Diversion Dam, and approximately 200 m (656 ft) downstream of the first footbridge and photo point 3 (Figures 3-20 and 3-21). During the 160 cfs flow release, the extent of the pool below the spillway increased slightly compared with the 50 cfs flow release, and pool depth increased by about 0.3 m (1 ft) relative to the 50 cfs flow release. At photo point 1, the water velocity in the pool increased slightly compared with the 50 cfs flow release, although velocity remained relatively low. Vegetation along the margins became increasingly inundated. At photo point 2, water depth was estimated to be approximately 0.3 m (1 ft) deeper than observed during the 50 cfs flow release; the channel remained too deep to wade. Wetted channel width at photo point 2 increased to approximately 54 m (177 ft) and inundation of vegetation and woody debris along the channel margins increased. At 160 cfs, the downstream extent of surface flow was shallow with no discernable water velocity (Appendices E and F). At this discharge, the stage recorder near photo point 3 (Figure 3-20) was just becoming wet, although it recorded zero water depth. 59

72 cfs flow release Under a 250 cfs flow release, continuous flow extended 2,795 m (9,170 ft) downstream of Carmen Diversion Dam (Figures 3-20 and 3-21) to the vicinity of photo point 4. At photo point 3, flow under the first footbridge was steady (Appendix F) and the stage recorder measured a maximum water depth of 0.44 m (1.44 ft). Stream discharge attenuated downstream from photo points 3 to 4, and surface flow ended near photo point 4. At this release, a small amount of water was observed discharging into Blue Pool near the base of Tamolitch Falls cfs flow release The 330 cfs flow release observation was conducted during a 22-day outage related to a safety inspection on the Carmen power tunnel and major maintenance at the Carmen Powerhouse. Rather than route the water over the Smith spillway, EWEB chose to divert the water into the upper Carmen Bypass Reach in October 2003 to permit study of the reach hydrology. During this observation, surface flow was continuous until some point between photo points 5 and 6, and standing water was intermittent between photo points 6 and 7, but surface water was not observed as far downstream as photo point 8 at any time during the spill (Figure 3-21). Under the 330 flow release, the downstream extent of surface flow was 3,409 m (11,184 ft) from Carmen Diversion Dam. At this release, water discharged into Blue Pool near the base of Tamolitch Falls. 3.6 Habitat Availability in Reservoirs Fish habitat availability in the three Project reservoirs was estimated using habitat criteria based on associations between fish distribution and physical habitat characteristics within the reservoirs. Fish distribution surveys generally indicated that: (1) most fish occurred in water less than 6 m (20 ft) deep, (2) few fish were present in water greater than 9 m (30 ft) deep, and (3) no fish occurred deeper than about 30 m (100 ft). Very little information was found during a literature review of reservoir habitat classification and reservoir habitat utilization by bull trout, Chinook salmon, or cutthroat trout. In Trail Bridge Reservoir, the comparison of substrate and cover types with fish distribution surveys indicated that fish distribution appears to be influenced more by water depth and bank slope than by substrate and cover types. Chinook salmon fry were most abundant in areas with shallow water (< 6 m [20 ft]), and low gradient bank slopes extending more than 30.5 m (100 ft) from shore. Fry were observed during both day and night in shallow water habitat, and were generally associated with vegetation. Bull trout fry were not observed in Trail Bridge Reservoir; however, unidentified char fry were observed in the Smith River arm of Trail Bridge Reservoir but could not be identified to species. Juvenile bull trout were commonly observed in areas with high abundance of Chinook salmon fry and seemed to be holding in water only a few feet beyond (i.e., toward deeper water) the distribution of Chinook salmon fry. Chinook salmon fry and juvenile bull trout were rarely observed in areas with steep bank gradients (> 50% measured from 0 6 m [0 20 ft]). The exception to this was the McKenzie River arm of Trail Bridge Reservoir, which was considered to be more riverine in character due to the flow contributed from the McKenzie River and the Carmen Powerhouse. Both sub-adult and adult bull trout were observed throughout the reservoir. These larger fish occurred most often near areas where smaller prey fish were observed, and where Sweetwater Creek enters the reservoir. Bull trout have been found in other reservoirs 60

73 associated with similar habitats and associated with prey (Bjornn 1961 as cited in McPhail and Baxter 1996, Goetz 1989). A few cutthroat trout were observed scattered throughout most parts of Trail Bridge Reservoir, but large numbers of cutthroat were only observed in the Smith River arm and adjacent to the boat ramp (north bank). In Smith Reservoir, which inundates a steep-sided canyon, most fish were distributed in the upstream (northern) portion of the reservoir where water is shallower, the reservoir is narrower, the bank slope is less steep, and where flows enter from the Smith River and the Carmen Diversion tunnel. Sonar surveys conducted in the reservoir detected 95% of the fish in water less than 15 m (50 ft) deep, and 100% of the fish in water less than 30 m (98 ft) deep. Fish trapping (frame traps) in Smith Reservoir captured one cutthroat trout and 12 rainbow trout (1 native and 11 hatchery). No fish were trapped at depths greater than 13 m (42 ft), and the single cutthroat trout was trapped at a depth of 30 ft. Oneida nets captured large numbers of fish but sampling was conducted in shallow water (< 3.3 m [10 ft]). Combined results from trapping (frame traps) and Oneida net surveys in Smith Reservoir indicate that approximately 73% of fish in the reservoir are hatchery rainbow or brook trout, 16% are cutthroat trout, 10% are mountain whitefish, and 1% is native rainbow trout. A detailed description of methods and results for sonar surveys and trapping studies is presented in the Fish Population Distribution and Abundance technical report (Stillwater Sciences 2006c). In Carmen Diversion Reservoir, direct observation surveys indicate that fish were widely distributed. Brook trout occurred mostly in the calmer waters of the reservoir s southern portion and near the margins of the north end. Both hatchery rainbow and cutthroat trout were most abundant in the northern portion of the reservoir where the influence of the McKenzie River flow through the reservoir is strongest. Fish distribution and habitat characteristics for suitable habitat were summarized (Table 3-40). Table Summary of fish habitat utilization in Project reservoirs. Species and life stage Chinook salmon fry 1 Reservoir habitats in which fish were most abundant Shallow margin habitats Chinook In shallow waters < 6 salmon Juveniles 1 m (20 ft deep) Bull trout fry 1 Bull trout juveniles 1 Not observed in reservoir In shallow waters < 6 m (20 ft deep) that extend > 30 m (100 ft) from shore Reservoir habitats in which fish were not observed Greater than 3 m (10 ft) deep, or where bank gradient 50% (measured from 0 6 m [0 20 ft]) Where bank gradient 50% (measured from 0 6 m [0 20 ft]) Not observed in reservoir Where bank gradient 50% (measured from 0 6 m [0 20 ft]), and in open water over deep sections of the reservoir Notes Often found in areas with large rip-rap and in shallow, low gradient areas with cover. Five unidentified char fry were observed in the Smith arm of Trail Bridge Reservoir in water < 2 m (5 ft) deep. Juvenile bull trout distribution generally occurred where Chinook salmon fry were abundant. 61

74 Species and life stage Bull trout adult and subadults 1 Coastal cutthroat trout 2 Reservoir habitats in which fish were most abundant In and around areas where smaller prey fish are present (i.e., shallow waters that extend from shore) Shallow water influenced by river flows 1 Fish observations only occurred in Trail Bridge Reservoir. 2 Fish observations occurred in all three Project reservoirs. Reservoir habitats in which fish were not observed In open water over deep sections of the reservoir In open water over deep sections of the reservoir Notes Sub-adults are thought to be using the entire reservoir and concentrating in areas where prey is abundant (Bjornn 1961, as cited in McPhail and Baxter 1996; Goetz 1989). The habitat criteria developed to define suitable habitat in the three project reservoirs are summarized (Table 3-41). These criteria were based on habitat characteristics in areas where greater than 95% of fish were observed, and exclude habitat characteristics of areas in which no fish were observed (e.g., areas 50% bank slope, measured from 0 6 m [0 20 ft]). Table Habitat criteria developed for mapping suitable habitat in reservoirs. Species and life stage Chinook salmon fry Chinook salmon juvenile Bull trout fry Juvenile bull trout Sub-adult and adult bull trout 1 Cutthroat trout adults Habitat criteria Water depth < 3 m (10 ft) 50% bank gradient to 6 m (20 ft) Water depth < 6 m (20 ft) Water depth < 3 m (10 ft) 50% bank gradient to 6 m (20 ft) Water depth < 6 m (20 ft) Water depth < 15 m (50 ft) Water depth < 15 m (50 ft) Based on the suitable habitat criteria, available habitat areas were calculated using GIS for the three Project reservoirs (Tables 3-42 and 3-43, Figures 3-22a b); maps were generated for Trail Bridge and Smith reservoirs (Figures 3-23a d). In addition, the amount of available habitat area common between high and low pool for Trail Bridge and Smith reservoirs was calculated (Tables 3-42 and 3-43), and can be spatially identified by comparing Figures 3-23a with 3-23b for Trail Bridge Reservoir, and Figures 3-22c with 3-22d for Smith Reservoir. In Trail Bridge Reservoir, estimated habitat area for bull trout and Chinook salmon juvenile, bull trout adult and subadult, and adult cutthroat adult were lowest at low pool (2,078 ft), and habitat area generally increased linearly as reservoir elevation rose to high pool (2,090 ft); high pool corresponded to the highest estimated habitat area. For bull trout and Chinook salmon fry rearing, habitat area was relatively stable. In Smith Reservoir, bull trout and Chinook salmon fry estimated habitat area was the greatest when the reservoir was at low pool elevation (2,593 ft), and habitat area generally decreased linearly as reservoir elevation rose to high pool (2,605 ft). For the other species and life stages, habitat area in Smith Reservoir was the smallest at low pool, but increased linearly as pool 62

75 elevation increased, until the greatest habitat area was obtained at full pool. In Carmen Diversion Reservoir, cutthroat trout adult were the only species and life stage for which habitat availability was assessed. Based on their selected habitat criteria, all of the reservoir (112,799 m 2 [1,214,158 ft 2 ]) provided suitable habitat, although mostly brook and hatchery trout were found in the reservoir. Species Table Summary of available habitat area in Trail Bridge Reservoir. Life stage Available habitat area at low pool (2,078 ft) Available habitat area at high pool (2,090 ft) Amount of available habitat area common between high and low pool m 2 ft 2 m 2 ft 2 m 2 ft 2 Chinook Fry 6,972 75,050 6,835 73, salmon Juvenile 90, , ,180 1,304,375 55, ,500 Fry 6,972 75,050 6,835 73, Juvenile 90, , ,180 1,304,375 55, ,500 Bull trout Coastal cutthroat trout Subadult 209,297 2,252, ,940 2,668, ,269 1,961,925 Adult 209,297 2,252, ,940 2,668, ,269 1,961,925 Adult 221,790 2,387, ,461 3,094, ,790 2,387,325 Species Table Summary of available habitat area in Smith Reservoir. Life stage Available habitat area at low pool (2,593) Available habitat area at high pool (2,605) Amount of available habitat area common between high and low pool m 2 ft 2 m 2 ft 2 m 2 ft 2 Chinook Fry 20, ,625 9,007 96, salmon Juvenile 114,338 1,230, ,982 1,678,975 53, ,725 Fry 20, ,625 9,007 96, Juvenile 114,338 1,230, ,982 1,678,975 53, ,725 Bull trout Coastal cutthroat trout Subadult 232,014 2,497, ,252 3,188, ,633 2,084,575 Adult 232,014 2,497, ,252 3,188, ,633 2,084,575 Adult 343,142 3,693, ,162 4,458, ,574 3,353,750 In addition to the species and life stages discussed above, habitat availability for juvenile Pacific lamprey and western brook lamprey were assessed in Project reservoirs based on the habitat criteria for these species and life stages (Table A-3). No juvenile lamprey habitat was identified in Project reservoirs. Although suitable substrates exist, water velocity in areas with suitable substrates was too low. 63

76 3.7 Corroboration of Habitat Mapping Approach Direct observations Fish locations identified during direct observation snorkel surveys were compared with available habitat mapped during the pilot mapping effort, to evaluate guild criteria definitions and the accuracy of the habitat mapping approach. Both qualitative and quantitative evaluations were used to compare the data sets. The qualitative evaluation was conducted prior to acceptance of the full habitat mapping approach and included a visual assessment of the accuracy and applicability of the mapping approach, considering habitat characteristics discernable from the photographic base maps (Appendix H). The visual assessment provided evidence that the habitat mapped was related to the locations of fish observations; evidence was sufficient to proceed with the approach for the full study. The quantitative evaluation included determining the likelihood that fish observations were located within the suitable habitat polygons (inside-outside test), and the likelihood that fish were closer to suitable habitat than not (proximity test) (see Section ) (Table 3-44 and Appendix H). Table Summary of results for the quantitative comparison testing the likelihood that fish observations were within suitable habitat areas mapped (inside-outside test), and the likelihood fish were closer to suitable habitat areas than not (proximity test). Tests significant at alpha = 0.05 are emphasized in bold text. Guild Sample size (n) Carmen Bypass Reach Smith Bypass Reach Habitat unit 6 Habitat unit 7 Habitat unit 34 Significance (alpha) Insideoutside test Proximity test Sample size (n) Significance (alpha) Insideoutside test Proximity test Sample size (n) Significance (alpha) Insideoutside Test Proximity test Chinook salmon fry NA 1 NA 1 0 NA 1 NA 1 rearing Coastal cutthroat trout 10 < adult Salmonid juvenile 23 < < < < NA 1 NA 1 Trout and char fry rearing 0 NA 1 NA Fish were not observed during direct observation surveys. Overall, the locations of fish observations corroborated a strong association with the locations of the suitable habitat areas mapped. Fish observation locations generally fell within, or near, the suitable habitat areas mapped. Larger sample sizes had especially strong correlations. Three of the ten comparisons with low sample size (n 3) were significant, suggesting that fish were observed in locations associated with the suitable habitat area mapped. Sample sizes were low (n 3) in all tests not significant at a 95% confidence level. 64

77 3.7.2 Two-dimensional (2D) modeling Results from the 2D modeling effort corroborated the habitat criteria mapping approach, and were used to select flows for conducting habitat criteria mapping during the full study. The mapping results spatial patterns were visually assessed to compare the habitat criteria mapping results with the 2D modeling results, prior to accepting the approach for the full study. Comparison of the 2D modeling with the habitat mapping suggests a strong correlation between the two methods (Appendix I). However, 2D model results should not be used to estimate habitat availability at flows that were not empirically mapped because (1) the 2D modeling and the habitat criteria approach were conducted together in only one habitat unit (lower Carmen Bypass Reach, habitat unit 6), which is hydraulically simple relative to most of the reach, and (2) results from the two methods indicate different spatial patterns of suitable habitat for some life stages and flows in this habitat unit (Figures 3-24a d). The greatest differences between the two methods are likely due to the 2D model s inability to accurately model suitable habitat along channel margins, where coarse substrates (i.e., roughness elements) increasingly affect water velocity. Due to the relatively high water velocities occurring in the lower Carmen Bypass Reach, the areas that the 2D model cannot accurately see are the areas where gravel patches develop and where most of the suitable habitat was mapped for all species life stages. Therefore, 2D model results are not appropriate surrogates for the habitat mapping results Evaluating mapping precision Results from the repeated mapping conducted by independent crews during the pilot mapping effort were assessed qualitatively. A visual comparison suggested that results from the repeated mapping surveys were relatively consistent between the different crews for guilds mapped in habitat units 7 and 34 in the Smith Bypass Reach, even though flow conditions varied during the period that the repeated mapping surveys were conducted. During the full mapping study, repeated mapping surveys were conducted at one flow (160 cfs) in the lower Carmen Bypass Reach, and at three flows (7, 85, and 120 cfs) in the Smith Bypass Reach, for a total of 28 comparisons (Appendix J). Results from the repeated mapping surveys were assessed quantitatively to provide an estimate of mapping precision. The Delta Method assessment described in Section yielded a symmetric interval of ± 30% for the mean percent difference of estimated areas between crews. This measure is not reported in other studies and therefore, it is difficult to compare this with other methods. 3.8 Flow Impacts on Macroinvertebrate Community Characteristics The two main effects that flow alterations can have on the macroinvertebrate community are: (1) displacement of immature stages or scouring of food resources by episodic high flow events that occur outside the time frame of the normal (historical) storm patterns, particularly those associated with high discharge spills during periods of naturally low flows, and (2) desiccation of immobile species in dewatered habitats following both natural and Project-induced flow fluctuation events. Reduced flows associated with Project operations may also affect macroinvertebrate communities. Both phenomena may cause shifts in community composition and abundance, and potentially affect the macroinvertebrate prey base for juvenile salmonids. Typically, invertebrates are most sensitive to non-natural flow regimes during emergence, oviposition, and hatching (early instars or stages); these life stage periods occur: (1) from 65

78 approximately mid-august through mid-october for taxa with fall-winter generations, and (2) from approximately May through June for taxa with spring-summer generations. Although transition times, which occur outside the periods given above, are not the ideal period to survey stream invertebrate populations, both fall-winter (full grown) and spring-summer (early instars) generations of invertebrate life history stages were observed and documented in May 2005 (Tables K-1 K-6). However, many aquatic invertebrates undergo several generations during the year and are not necessarily limited to specific time frames. Rearing phases, such as nymphs, larvae, and pupae that reside on the stream bottom for extended periods, could also be greatly affected by flow alterations. The ecosystem attribute indices for the May 2005 qualitative survey and the 1999 and 2004 macroinvertebrate surveys are described below, and summarized in Tables K-7 K Autotrophy/heterotrophy index In 2005, the Autotrophy/Heterotrophy Index, or P/R (primary production divided by community respiration) ratio, was 0.07 in Sweetwater Creek, indicating low algal production and a heterotrophic system. The autotrophic components that were present, such as moss, filamentous algae, and vascular hydrophytes, are not suitable food for scrapers (Table K-6). In 2005, the P/R ratio was 0.65 in the Smith Bypass Reach, indicating algal production was significant with periphyton on the cobbles, but the system was still heterotrophic. Based on these observations, the major energy source for macroinvertebrates in the Smith Bypass Reach is riparian litter or fine particulate organic matter (FPOM) from Bunchgrass Creek (Table K-4). In 2005, the P/R ratio was 1.61 in the lower Carmen Bypass Reach, indicating an autotrophic system driven by algal production by extensive periphyton cover (Table K-2); however, in 2004 the ratio was low at both the lower Carmen Bypass Reach and the McKenzie River sites, suggesting production was heterotrophic. In the 1999 and 2004 samples taken upstream and downstream of Smith Reservoir, the invertebrate surrogate P/R ratio indicated algal production was low and that the Smith Bypass Reach was heterotrophic in both years, but the ratio indicated the Smith River was autotrophic in 1999 (Tables K-11 K-18) Shredder-riparian index In the May 2005 macroinvertebrate survey, shredders were found at all three stream sites sampled: Sweetwater Creek, Smith Bypass Reach, and lower Carmen Bypass Reach (Tables K- 1 K-6). However, in 2005, only the unregulated, groundwater-dominated Sweetwater Creek met the expected threshold value for the invertebrate surrogate ratio CPOM/FPOM, indicating a normal riparian-shredder linkage. Shredders may have been underrepresented in the samples from the lower Carmen Bypass Reach and Smith Bypass Reach sites because of the sampling time. In 2005, the shredders present were primarily large, full-grown limnephilid caddisfly larvae of fall-winter generations; these fall-winter shredders were at the end of their growth period and spring-summer shredders were in adult and egg stages or very small early instars. In the 1999 and 2004 samples, shredders were found at all sites sampled (Tables K-7 K-18); however, the collections were taken in riffles, which likely resulted in lower ratios than if samples had been taken closer to channel margins in litter accumulations. Only the McKenzie River and lower Carmen Bypass Reach sites, and the Smith Bypass Reach site in 2004, exhibited invertebrate surrogate ratios (CPOM/FMPOM) above the expected threshold for a normal coupling between riparian litter supply and fall-winter shredders. 66

79 3.8.3 Suspended load index Filtering collectors were present in low numbers, whereas gathering collectors were numerous at all riverine sites surveyed in all years (Tables K-1 K-18). The ratio of transported fine particulate organic matter to the benthic fine particulate organic matter (TFPOM/BFPOM) surrogate suspended load index was very low at all sites, including the sites upstream and downstream of Smith Reservoir, sampled in 2004 and 1999, and in the McKenzie River upstream and downstream of Carmen Diversion Reservoir in 2004, suggesting that the quantity and/or quality of FPOM in transport was low in the area, regardless of the Project Stability index Even though Smith Bypass Reach is prone to episodic high flow events, both natural and infrequently from spill at Smith Dam, scrapers were abundant in the Smith Bypass Reach and the lower Carmen Bypass Reach sites in 2005, accounting for over 30% of the total invertebrates at these sites; however, scrapers accounted for only 6% of the invertebrate composition at Sweetwater Creek (Tables K-1 K-6). Although Sweetwater Creek has stable, unregulated flows, the habitat stability index was low, likely due to moss that covers surfaces and excludes scrapers. The stability index was high for both the lower Carmen Bypass Reach and Smith Bypass Reach sites in 2005, suggesting that flows and substrate are suitably stable to support less mobile taxa. However, in the 1999 and 2004 samples, scrapers were generally a smaller proportion of the total invertebrates in both the Smith River and Smith Bypass Reach, suggesting that habitat stability was lower in 1999 and 2004 than in 2005 (Tables K-11 K-18) Juvenile salmonid food index Although flow alterations may influence macroinvertebrate community composition, the data collected for this study indicate little effect on potential juvenile salmonid prey availability. The behavioral/accidental drift approximation ratios for the samples taken on 9 10 May 2005 suggest that salmonid prey availability was very good in the Smith Bypass Reach and in Sweetwater Creek, but very poor in the lower Carmen Bypass Reach (Tables K-1 K-6). The ratios for 2005 are approximated because they were determined based on field sorting rather than examination of macroinvertebrates in the laboratory by dissecting microscopy, as was done for surveys conducted in 1999 (Aquatic Biology Associates, Inc. 1999) and 2004 (Stillwater Sciences 2006e). The behavioral/accidental drift ratios from samples taken in 2004 indicate good salmonid prey availability in the Smith River and the Smith Bypass Reach, and in the McKenzie River and lower Carmen Bypass Reach (Tables K-7 K-14). In 1999, the salmon prey availability index was higher in the Smith Bypass Reach than in the Smith River above Smith Reservoir (Tables K-15 K-18). In summary, flow and habitat conditions for macroinvertebrates under existing conditions appear to provide good salmonid prey availability in the Smith Bypass Reach and Sweetwater Creek, and poor prey availability in the lower Carmen Bypass Reach. Poor prey availability in the lower Carmen Bypass Reach may be related to the spill from Carmen Diversion Dam that increased flows for habitat mapping from baseflows of approximately 175 cfs, to 345 cfs on 6 10 May

80 4 LITERATURE CITED Addley, C. R., B. Bradford, M. Combes, S. Clemens, and M. Winkelaar Two-dimensional habitat modeling draft. Carmen-Smith Hydroelectric Project (FERC No. 2242). Draft report. Prepared by Institute of Natural Systems Engineering, Utah State University, Utah Water Research Laboratory, Logan Utah for Stillwater Sciences, Arcata, California. Aquatic Biology Associates, Inc Benthic invertebrate biomonitoring for the McKenzie River Watershed Council, Oregon, September-October Prepared for Willamette National Forest, Blue River and McKenzie River Ranger Districts, Blue River, Oregon by Aquatic Biology Associates, Inc., Corvallis, Oregon. Baxter, C. V., and F. R. Hauer Geomorphology, hyporheic exchange, and selection of spawning habitat by bull trout (Salvelinus confluentus). Canadian Journal of Fisheries and Aquatic Sciences 57: Baxter, J. S., and J. D. McPhail The influence of redd site selection, groundwater upwelling, and over-winter incubation temperature on survival of bull trout (Salvelinus confluentus) from egg to alevin. Canadian Journal of Zoology 77: Bjornn, T. C Harvest, age structure, and growth of game fish populations from Priest and upper Priest lakes. Transactions of American Fisheries Society 90: Bonneau, J. L Seasonal habitat use and changes in distribution of juvenile bull trout and cutthroat trout in small, high gradient streams. Master's thesis. University of Idaho, Moscow. Bowman, A. W., and A. Azzalini Applied smoothing techniques for data analysis: the kernel approach with S-Plus illustrations. Oxford Statistical Science Series No. 18. Clarendon Press, Oxford, England. Cochran, W. G Sampling techniques. 3rd edition. John Wiley & Sons, New York. Cummins, K. W., and M. J. Klug Feeding ecology of stream invertebrates. Annual Review of Ecology and Systematics 10: EWEB (Eugene Water & Electric Board) Initial consultation package for relicensing the Carmen-Smith Hydroelectric Project (FERC No. 2242). Final report. Prepared by Stillwater Sciences, Arcata, California for EWEB, Eugene, Oregon. FERC (Federal Energy Regulatory Commission) Order approving conservation measures and requiring study plans and reports with respect to threatened and endangered species (issued August 1, 2003). Eugene Water & Electric Board, Project No FERC 62,080. Ghanem, A., P. Steffler, F. Hicks, and C. Katopodis Two-dimensional hydraulic simulation of physical habitat conditions in flowing streams. Regulated Rivers: Research and Management 12: Goetz, F Biology of the bull trout, Salvelinus confluentus, a literature review. USDA Forest Service, Willamette National Forest, Eugene, Oregon. 68

81 Goetz, F Distribution and juvenile ecology of bull trout (Salvelinus confluentus) in the Cascade Mountains. Master's thesis. Oregon State University, Corvallis. Hauer, F. R., and V. H. Resh Chapter 16. Benthic macroinvertebrates. Pages in F. R. Hauer and G. A. Lamberti, editor. Methods in stream ecology. Academic Press, San Diego, California. Hawkins, C. P., J. L. Kershner, P. A. Bisson, M. D. Bryant, L. M. Decker, S. V. Gregory, D. A. McCullough, C. K. Overton, G. H. Reeves, R. J. Steedman, and M. K. Young A hierarchical approach to classifying stream habitat features. Fisheries 18: Jakober, M. J Influence of stream size and morphology on the seasonal distribution and habitat use of resident bull trout and westslope cutthroat trout in Montana. Master's thesis. Montana State University, Bozeman. Jefferson, A., G. Gordon, and T. Rose. 2006, in preparation. Residence times and recharge of groundwater in volcanic aquifers in Oregon High Cascades. LeClerc, M., A. Boudreault, J. A. Bechara, and G. Corfa Two-dimensional hydrodynamic modeling: a neglected tool in the Instream Flow Incremental Methodology. Transactions of the American Fisheries Society 124: Manly, B. F. J Randomization, Bootstrap, and Monte Carlo methods in biology. Second edition. Chapman & Hall, London. McBain and Trush Estimating salmonid habitat availability in the lower Oak Grove Fork using expert habitat mapping: summary of methods and preliminary results. Prepared for Clackamas Instream Flow/Geomorphology Subgroup, Portland General Electric, Portland, Oregon by McBain and Trush, Arcata, California. McPhail, J. D., and J. S. Baxter A review of bull trout (Salvelinus confluentus) life-history and habitat use in relation to compensation and improvement opportunities. Fisheries Management Report No University of British Columbia, Department of Zoology, Vancouver. Merritt, R. W., and K. W. Cummins An introduction to the aquatic insects of North America. Kendall/Hunt Publishing Company, Dubuque, Iowa. Merrit, R. W., K. W. Cummins, M. B. Berg, J. A. Novak, M. J. Higgins, K. J. Wessell, and J. L. Lessard Development and application of a macroinvertebrate functional- group approach in the bioassessment of remnant river oxbows in southwest Florida. Journal of the North American Benthological Society 21: Mohr, M. S., and D. G. Hankin Two-phase survey designs for estimation of fish abundance in small streams. Draft Report. Prepared by NOAA Fisheries, Southwest Fisheries Science Center(SWFSC), Santa Cruz Laboratory, Santa Cruz, California and Department of Fisheries Biology, Humboldt State University, Arcata, California. Montgomery, D. R., and J. M. Buffington Channel-reach morphology in mountain drainage basins. Geological Society of America Bulletin 109:

82 Montgomery, D. R., J. M. Buffington, R. D. Smith, K. M. Schmidt, and G. Pess Pool spacing in forest channels. Water Resources Research 31: Murphy, M. L., and K. V. Koski Input and depletion of woody debris in Alaska streams and implications for streamside management. North American Journal of Fisheries Management 9: NOAA Fisheries Biological opinion and Magnuson-Stevens Fishery Conservation and Management Act consultation on the effects of EWEB's Carmen-Smith Part 12 submittal to FERC for Trail Bridge Dam emergency spillway expansion, and continued operation of the Carmen-Smith Hydroelectric Project in the McKenzie Subbasin, Oregon on Upper Willamette River Chinook salmon. Prepared for Federal Energy Regulatory Commission, Washington, D. C. ODEQ (Oregon Department of Environmental Quality) Beneficial uses of the state's waters. ODEQ, Portland, Oregon. ODFW (Oregon Department of Fish and Wildlife) McKenzie River spring chinook salmon distribution map. ODFW, Portland. Richmond, A. D., and K. D. Fausch Characteristics and function of large woody debris in subalpine Rocky Mountain streams in northern Colorado. Canadian Journal of Fisheries and Aquatic Sciences 52: R2 Resource Consultants, Inc Pit River habitat mapping: results of the August 2002 demonstration flow study. Final Report. Prepared by R2 Resource Consultants, Inc., Redmond, Washington for Pacific Gas and Electric Company, Technical and Ecological Services. Steffler, P., and J. Blackburn River 2D: two-dimensional depth averaged model of river hydrodynamics and fish habitat. Introduction to depth averaged modeling and user's manual. Prepared by University of Alberta. Stillwater Sciences. 2004a. Aquatic Habitats and Instream Flows. Final study plan for the Carmen-Smith Hydroelectric Project relicensing (FERC No. 2242). Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. Stillwater Sciences. 2004b. Carmen Diversion Dam 2003 maintenance spill. Technical Memorandum. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. Stillwater Sciences. 2004a. Aquatic habitats and instream flows. Final study plan for the Carmen- Smith Hydroelectric Project relicensing (FERC No. 2242). Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. Stillwater Sciences. 2006b. Hydrologic regimes in the Carmen-Smith Hydroelectric Project area, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. Stillwater Sciences. 2006c. Fish population distribution and abundance in the Carmen-Smith Hydroelectric Project area, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. 70

83 Stillwater Sciences. 2006d. Aquatic protection, mitigation, and enhancement opportunities in the Carmen-Smith Hydroelectric Project area, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. Stillwater Sciences. 2006e. Water quality in the Carmen-Smith Hydroelectric Project area, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. Stillwater Sciences. 2006f. Fish entrainment in the Carmen-Smith Hydroelectric Project area, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon. Thurow, R. F., and D. J. Schill Comparison of day snorkeling, night snorkeling, and electrofishing to estimate bull trout abundance and size structure in a second-order Idaho stream. North American Journal of Fisheries Management 16: ULEP (Umpqua Land Exchange Project) Mapping rules for Chinook salmon (Oncorhynchus tshawytscha). Draft Report. ULEP, Roseburg, Oregon. USFWS (U. S. Fish and Wildlife Service) Biological/conference opinion on the effects of EWEB's Carmen-Smith Part 12 submittal to FERC for Trail Bridge spillway expansion, and interim operation of the Carmen-Smith Hydroelectric Project in the McKenzie Subbasin, Oregon on bull trout, bald eagle, and northern spotted owl. Endangered Species Act - Section 7 (a)(2) Consultation; USFWS Log No F-455. Prepared for Federal Energy Regulatory Commission by USFWS, Oregon Fish and Wildlife Office. Wilzbach, M. A., K. W. Cummins, T. K. Barnes, and J. C. Trexler Channel- floodplain coupling inthe Kissimmee River, Florida (USA): invertebrate movement and fish feeding. Verhandlungen der Internationalen Vereinigung fur Theoretische und Angewandte Limnologie 28: Wilzbach, M. A., K. W. Cummins, and J. D. Hall Influence of habitat manipulations on interactions between cutthroat trout and invertebrate drift. Ecology 67: Wolman, G. M A method of sampling coarse river-bed material. Transactions of the American Geophysical Union 35: Xu, J., and J. S. Long Using the Delta Method to construct confidence intervals for predicted probabilities, rates, and discrete changes in Confidence intervals for predicted outcomes in regression models for categorical outcomes. Submitted to The Stata Journal. 71

84 FIANL REPORT Carmen-Smith Hydroelectric Project (FERC No. 2242) Figures

85 Hydrologic Regimes RIVER CHANNEL DYNAMICS Sediment Budget Large Woody Debris Dynamics AQUATIC HABITAT CONDITIONS Water Quality Fluvial Geomorphic Processes and Channel Morphology Aquatic Habitats and Instream Flows Aquatic Habitat Connectivity FISHERIES BOTANY AND WILDLIFE SOCIAL SCIENCES Fish Population Distribution and Abundance Vegetation and Wetland Mapping and Characterization Historical and Archaeological Resources Entrainment Botanical Field Surveys Existing Recreational Uses Flow Fluctuations and Stranding Wildlife Distribution Recreation Suitability Population Dynamics of Bull Trout and Spring Chinook Salmon Wildlife Analyses Whitewater Boating Feasibility Fish Passage Feasibility Aesthetic Resources Aquatic Protection, Mitigation, and Enhancement Opportunities License Application Land Use and Management Figure 1-1. Relationship of the Aquatic Habitats and Instream Flows study to other Carmen-Smith Hydroelectric Project relicensing studies.

86 Figure 1-2. Study Area.

87 Figure 2-1. Photo point locations in the lower Carmen Bypass Reach.

88 Figure 2-2. Photo point locations in the upper Carmen Bypass Reach.

89 Figure 2-3a. Distribution of cover types used for 2D modeling in lower Carmen Bypass Reach habitat unit 6.

90 Figure 2-3b. Distribution of cover types used for 2D modeling in Smith Bypass Reach habitat unit 7.

91 Figure 2-3c. Distribution of cover types used for 2D modeling in Smith Bypass Reach habitat unit 34.

92 Figure 2-4. Macroinvertebrate sampling sites in the Study Area.

93 Figures 2-5a-b. Inundation zone of Trail Bridge Reservoir (a) and macroinvertebrate sampling using D-frame kicknet within the McKenzie River downstream of Trail Bridge Dam (b).

94 Figure 2-6. Field sorting of macroinvertebrates.

95 Figure 3-1a. Annual hydrograph for the lower Carmen and Smith bypass reaches under current conditions based on synthetic hydrologic record from 1 October 1960 to 21 July Life history timing for bull trout based on distribution data from the lower Carmen Bypass Reach is indicated above the chart. Spawning Late fry rearing Bull Trout Early fry rearing Adult, subadult, and juvenile Spawning Late fry rearing Carmen Bypass Reach Smith Bypass Reach Carmen discharge (cfs) Smith discharge (cfs) Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Date 0

96 Figure 3-1b. Annual hydrograph for the lower Carmen and Smith bypass reaches under current conditions based on synthetic hydrologic record from 1 October 1960 to 21 July Life history timing for spring Chinook salmon based on distribution data from the lower Carmen Bypass Reach is indicated above the chart. 400 Spawning Juvenile rearing Spring Chinook Salmon Spawning Fry rearing Juvenile rearing Adult Carmen Bypass Reach Smith Bypass Reach Carmen discharge (cfs) Smith discharge (cfs) Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Date 0

97 Bull trout spawning Bull trout early fry rearing Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs) Bull trout late fry rearing Bull trout juvenile rearing Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs) Figure 3-2a-d. Available habitat area in the lower Carmen Bypass Reach estimated for bull trout spawning (a), early fry rearing (b), late fry rearing (c), and juvenile rearing (d). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. (Note: the y-axis scale is different for the spawning life stage)

98 Figure 3-3a-d. Available habitat area in the Smith Bypass Reach estimated for bull trout spawning (a), early fry rearing (b), late fry rearing (c), and juvenile rearing (d). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. (Note: the y-axis scale is different for the spawning life stage) Habitat area (m 2 ) Bull trout spawning Habitat area (m 2 ) Bull trout early fry rearing Discharge (cfs) Discharge (cfs) Bull trout late fry rearing Bull trout juvenile rearing Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs)

99 Chinook salmon spawning Chinook salmon fry rearing Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs) Chinook salmon juvenile rearing Habitat area (m 2 ) Discharge (cfs) Figure 3-4a-c. Available habitat area in the lower Carmen Bypass Reach estimated for Chinook salmon spawning (a), fry rearing (b), and juvenile rearing (c). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. (Note: the y-axis scale is different for the spawning life stage)

100 Chinook salmon spawning Chinook salmon fry rearing Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs) Chinook salmon juvenile rearing Habitat area (m 2 ) Discharge (cfs) Figure 3-5a-c. Available habitat area in the Smith Bypass Reach estimated for Chinook salmon spawning (a), fry rearing (b), and juvenile rearing (c). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. (Note: the y-axis scale is different for the spawning life stage)

101 Resident trout adult Resident trout spawning Discharge (cfs) Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Resident trout fry rearing Resident trout juvenile rearing Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs) Figure 3-6a-d. Available habitat area in the lower Carmen Bypass Reach estimated for resident trout adult (a), spawning (b), fry rearing (c), and juvenile rearing (d). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. (Note: the y-axis scale is different for the spawning life stage)

102 Resident trout adult Resident trout spawning Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs) Resident trout fry rearing Resident trout juvenile rearing Habitat area (m 2 ) Habitat area (m 2 ) Discharge (cfs) Discharge (cfs) Figure 3-7a-d. Available habitat area in the Smith Bypass Reach estimated for resident trout adult (a), spawning (b), fry rearing (c), and juvenile rearing (d). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. (Note: the y-axis scale is different for the spawning life stage)

103 Mountain whitefish fry rearing Habitat area (m 2 ) Discharge (cfs) Mountain whitefish juvenile rearing Habitat area (m 2 ) Discharge (cfs) Figure 3-8a-b. Available habitat area in the lower Carmen Bypass Reach estimated for mountain whitefish fry rearing (a) and juvenile rearing (b). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area.

104 Mountain whitefish fry rearing Habitat area (m 2 ) Discharge (cfs) Mountain whitefish juvenile rearing Habitat area (m 2 ) Discharge (cfs) Figure 3-9a-b. Available habitat area in the Smith Bypass Reach estimated for mountain whitefish fry rearing (a) and juvenile rearing (b). The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area.

105 Pacific lamprey spawning Habitat area (m 2 ) Discharge (cfs) Figure Available habitat area in the lower Carmen Bypass Reach estimated for Pacific lamprey spawning. The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. Pacific lamprey spawning Habitat area (m 2 ) Discharge (cfs) Figure Available habitat area in the Smith Bypass Reach estimated for Pacific lamprey spawning. The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area.

106 Western brook lamprey spawning Habitat area (m 2 ) Discharge (cfs) Figure Available habitat area in the lower Carmen Bypass Reach estimated for western brook lamprey spawning. The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area. Western brook lamprey spawning Habitat area (m 2 ) Discharge (cfs) Figure Available habitat area in the Smith Bypass Reach estimated for western brook lamprey spawning. The outer band (dark blue) represents the 90% confidence interval, the intermediate band (light blue) represents the 50% confidence interval, and the central line represents the estimated habitat area.

107 350 Detritus with other cover 300 Detritus cover only Cover with no detritus 250 Habitat area (m 2 ) Discharge (cfs) Detritus with other cover Detritus cover only Cover with no detritus 350 Habitat area (m 2 ) Discharge (cfs) Figure 3-14a-b. Relative amount of detritus cover types for the trout and char fry rearing guild in habitat units mapped in the Carmen Bypass Reach (a) and the Smith Bypass Reach (b).

108 Figure 3-15a-e. Comparison of habitat availability in the lower Carmen Bypass Reach for habitat units having relatively high wood loading (blue) to habitat units with relatively low wood loading (red). The outer extent of the dark band represents the 90% confidence interval, the outer extent of the light band represents the 50% confidence interval, and the central line represents the estimate of habitat availability in the reach. (Note: the y-axis scale varies to improve resolution) Cutthroat Trout Adult Guild Adult Resident Trout Spawning Guild Habitat area (m 2 )/stream length (m) Discharge (cfs) Discharge (cfs) Habitat area (m 2 )/stream length (m) Bull Trout Spawning Guild Trout and Char Fry Rearing Guild Habitat area (m 2 )/stream length (m) Habitat area (m 2 )/stream length (m) Discharge (cfs) Discharge (cfs) Salmonid Juvenile Rearing Guild Habitat area (m 2 )/stream length (m) Discharge (cfs)

109 Figure 3-16a-e. Comparison of habitat availability in the lower Carmen Bypass Reach for habitat units having relatively high wood loading (blue) to habitat areas mapped during the criteria mapping effort (red). The outer extent of the dark band represents the 90% confidence interval, the outer extent of the light band represents the 50% confidence interval, and the central line represents the estimate of habitat availability in the reach. (Note: the y- axis scale varies to improve resolution) Cutthroat Trout Adult Guild Adult Resident Trout Spawning Guild Habitat area (m 2 )/stream length (m) Habitat area (m 2 )/stream length (m) Discharge (cfs) Discharge (cfs) Bull Trout Spawning Guild Trout and Char Fry Rearing Guild Habitat area (m 2 )/stream length (m) Habitat area (m 2 )/stream length (m) Discharge (cfs) Discharge (cfs) Salmonid Juvenile Rearing Guild Habitat area (m 2 )/stream length (m) Discharge (cfs)

110 Figure 3-17a-e. Comparison of habitat availability in the lower Carmen Bypass Reach for areas in close proximity to wood accumulations (blue) to areas not in close proximity to wood accumulations (red). The outer extent of the dark band represents the 90% confidence interval, the outer extent of the light band represents the 50% confidence interval, and the central line represents the estimate of habitat availability in the reach. (Note: the y- axis scale varies to improve resolution) Cutthroat Trout Adult Guild Adult Resident Trout Spawning Guild Habitat area (m 2 )/stream area (m 2 ) Habitat area (m 2 )/stream length (m) Discharge (cfs) Discharge (cfs) Habitat area (m 2 )/stream length (m) Bull Trout Spawning Guild Habitat area (m 2 )/stream length (m) Trout and Char Fry Rearing Guild Discharge (cfs) Discharge (cfs) Salmonid Juvenile Rearing Guild Habitat area (m 2 )/stream length (m) Discharge (cfs)

111 Bull trout Sweetwater Creek Adult Spawning Early fry rearing Late fry rearing Juvenile rearing Area (m) Area (m) 2 Life stage Bull trout Kink Creek Adult Spawning Early fry rearing Late fry rearing Juvenile rearing Life stage Figures 3-18a-b. Estimated available habitat area (m 2 ) for bull trout in Sweetwater Creek (a) and Kink Creek (b). Error bars represent 90% confidence interval.

112 Area (m) Bull trout Smith River above Smith Reservoir and Browder Creek Adult Spawning Early fry rearing Late fry rearing Juvenile rearing Life stage Chinook salmon Sweetwater Creek Area (m) Adult Spawning Fry rearing Juvenile rearing Life stage Figures 3-18c-d. Estimated available habitat area (m 2 ) for bull trout in Smith River above Smith Reservoir and Browder Creek (c) and for Chinook salmon in Sweetwater Creek (d). Error bars represent 90% confidence interval.

113 Chinook salmon Kink Creek Area (m) Adult Spawning Fry rearing Juvenile rearing Life stage Chinook salmon Smith River above Smith Reservoir and Browder Creek Area (m) Adult Spawning Fry rearing Juvenile rearing Life stage Figures 3-18e-f. Estimated available habitat area (m 2 ) for Chinook salmon in Kink Creek (e) and Smith River above Smith Reservoir and Browder Creek (f). Error bars represent 90% confidence interval.

114 Resident trout Sweetwater Creek Adult Spawning Fry rearing Juvenile rearing Area (m) Area (m) 2 Life stage Resident trout Kink Creek Adult Spawning Fry rearing Juvenile rearing Life stage Figures 3-18g-h. Estimated available habitat area (m 2 ) for resident trout in Sweetwater Creek (g) and Kink Creek (h). Error bars represent 90% confidence interval.

115 Area (m) Resident trout Smith River above Smith Reservoir Adult Spawning Fry rearing Juvenile rearing Life stage Mountain whitefish trout Sweetwater Creek Area (m) Fry rearing Juvenile rearing Life stage Figures 3-18i-j. Estimated available habitat area (m 2 ) for resident trout in Smith River above Smith Reservoir and Browder Creek (i) and for mountain whitefish in Sweetwater Creek (j). Error bars represent 90% confidence interval.

116 Mountain whitefish Kink Creek Fry rearing Area (m) 2 Juvenile rearing Area (m) Life stage Mountain whitefish Smith River above Smith Reservoir and Browder Creek Fry rearing Juvenile rearing Life stage Figures 3-18k-l. Estimated available habitat area (m 2 ) for mountain whitefish in Kink Creek (k) and in Smith River above Smith Reservoir and Browder Creek (l). Error bars represent 90% confidence interval.

117 Pacific lamprey Sweetwater Creek Area (m) 2 Area (m) Spawning Juvenile rearing Life stage Pacific lamprey Smith River above Smith Reservoir Spawning Juvenile rearing Life stage Figures 3-18m-n. Estimated available habitat area (m 2 ) for Pacific lamprey in Sweetwater Creek (m) and in Smith River above Smith Reservoir and Browder Creek (n). Error bars represent 90% confidence interval.

118 Western brook lamprey Sweetwater Creek Area (m) 2 Life stage Area (m) Spawning Juvenile rearing Western brook lamprey Smith River above Smith Reservoir and Browder Creek Spawning Juvenile rearing Life stage Figures 3-18o-p. Estimated available habitat area (m 2 ) for western brook lamprey in Sweetwater Creek (o) and in Smith River above Smith Reservoir and Browder Creek (p). Error bars represent 90% confidence interval.

119 Carmen Diversion Dam spill Discharge at the Clear Lake gage Flow release from Carmen Diversion Dam (cfs) Discharge at the Clear Lake gage (cfs) 0 27 Apr 1 May 5 May 9 May 13 May 17 May Date Figure Hydrograph of flow release from the Carmen Diversion Dam for habitat mapping efforts in the Carmen Bypass Reach in May

120 Distance downstream from dam (m) Distance downstream from dam Estimated available habitat area (m 2 ) Estimated available habitat area Flow release (cfs) Figure Distance that surface flow extends downstream of Carmen Diversion Dam and associated available habitat area estimated over a range of flow releases. 0

121 Figure Downstream extent of surface water from flow releases in the upper Carmen Bypass Reach.

122 300, ,000 Available habitat area (m 2 ) 200, , ,000 50,000 Bull trout adult and subadult Bull trout and Chinook fry rearing Bull trout and Chinook juvenile rearing Cutthroat trout adult Water surface elevation (ft) 450, , ,000 Available habitat area (m 2 ) 300, , , , ,000 50,000 Bull trout adult and subadult Bull trout and Chinook fry rearing Bull trout and Chinook juvenile rearing Cutthroat trout adult Water surface elevation (ft) Figures 3-22a-b. Estimated available habitat area for analysis species and life stages in Trail Bridge Reservoir (a) and Smith Reservoir (b) for the range of low to high pool water surface elevations under current Project operations.

123 Figure 3-23a. Habitat availability for analysis species in Trail Bridge Reservoir at low pool (2,078 ft) water surface elevation.

124 Figure 3-23b. Habitat availability for analysis species in Trail Bridge Reservoir at high pool (2,090 ft) water surface elevation.

125 Figure 3-23c. Habitat availability for analysis species in Smith Reservoir at low pool (2,593 ft) water surface elevation.

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