DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN. Prepared for: Squaxin Island Tribe Natural Resources Department September 2015

Transcription

1 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Prepared for: Squaxin Island Tribe Natural Resources Department 1 46 N Canal St, Suite 1 11 Seattle, WA com

2 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Prepared for: Squaxin Island Tribe Natural Resources Department 3110 Billy Frank Jr. Way Shelton, WA Authored by: Paul Schlenger, Chris Berger, and Lauren Odle Confluence Environmental Company Shane Cherry Shane Cherry Consulting 1 46 N Canal St, Suite 1 11 Seattle, WA com

3 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN TABLE OF CONTENTS 1 INTRODUCTION OVERVIEW OF WATERSHED SETTING SYNTHESIS OF COHO SALMON UTILIZATION OF DESCHUTES RIVER WATERSHED History of Salmon in Deschutes River Coho Salmon Population Trends EVALUATION OF HABITAT CONDITIONS Geomorphology of the Deschutes Basin Overview Geology Hydrology Sediment Supply and Transport Geomorphic Implications for Biological Recovery Salmon Habitat Limiting Factors Fish Passage Substrate Streambank Stability Large Woody Debris Pool Habitat Off-Channel Habitat Riparian Vegetation Buffers Water Quality Water Quantity Estuarine Habitat Deficiencies By Life Stage Adult Migration and Spawning Incubation and Emergence Spring and Summer Rearing Overwintering Smoltification RECOVERY STRATEGY Page i

4 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN 5.1 Identification of a Recovery Goal for Coho Salmon Types and Magnitude of Restoration Needed Restoration Scenarios Analysis Recommended Restoration Strategy Map and Database of Restoration Opportunities Estimated Quantity of Restoration Needed Placement of Large Wood to Form Instream Habitat Riparian Planting Bank Stabilization to Reduce Fine Sediment Inputs SUMMARY AND RECOMMENDATIONS REFERENCES TABLES Table 1. Type and Magnitude of Habitat Restoration in Restoration Scenario A Table 2. Target Large Wood Loading Quantities by River Reach Table 3. Estimated Implementation Costs for Deschutes Biological Recovery Plan FIGURES Figure 1. Vicinity Map Figure 2. Annual Number of Coho Adult Returns to the Deschutes River Since 1980 Figure 3. Recent Coho Adult Returns for Each Cohort Figure 4. Annual Number of Coho Adult Returns and Marine Survival Rate in the Deschutes River Figure 5. Shiraz Assessment Reaches Figure 6. Comparison of Shiraz Predictions and WDFW Observations of Annual Coho Adult Returns Figure 7. Predicted Coho Adult Returns in Restoration Scenario A and with the Continuation of Existing Conditions Figure 8. Predicted Coho Adult Returns in Restoration Scenario B which includes higher Marine Survival Figure 9. Examples of Priority Restoration Actions in the Deschutes River Watershed RM Figure 10. Examples of Priority Restoration Actions in the Deschutes River Watershed RM Figure 11. Examples of Priority Restoration Actions in the Deschutes River Watershed RM Figure 12. Examples of Priority Restoration Actions in the Deschutes River Watershed RM Figure 13. Examples of Priority Restoration Actions in the Deschutes River Watershed RM Page ii

5 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Figure 14. Examples of Priority Restoration Actions in the Deschutes River Watershed RM Figure 15. Examples of Priority Restoration Actions in the Deschutes River Watershed RM Figure 16. Examples of Priority Restoration Actions in the Deschutes River Watershed RM 7-12 Figure 17. Examples of Priority Restoration Actions in the Deschutes River Watershed RM 2-7 APPENDIX Appendix A. Shiraz Model Methods Page iii

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7 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN 1 INTRODUCTION Coho salmon returns to the Deschutes River have decreased markedly since the 1980s. In two of the three coho brood lines in the river, the decreased returns have been severe. In fact, WDFW (2012) describes the two lowest brood lines as virtually extinct. Thus, the Deschutes River coho population is vulnerable to be non-sustaining, especially when considering its ability to sustain through unfavorable cyclic conditions (e.g., El Nino and Pacific Decadal Oscillation) or climate change. Over the years, multiple studies have been conducted to provide information on habitat conditions in the watershed and assess specific relevant topics for understand the river processes in the watershed. More recently, there have also been assessments to help inform restoration planning efforts. But, to date, there has been only limited restoration actually implemented in the watershed. As the coho salmon population continues to return low numbers of returning adults, there is increased interest in implementing restoration and protection projects in the watershed. This Coho Salmon Biological Recovery Plan (Plan) was developed to help inform restoration and conservation specialists of the work needed in the watershed. The information provided through this analysis identifies the locations and types of habitat improvements needed. In addition, the Plan provides an estimate for the scale of the restoration work needed to recover a stable coho population in the basin. The analysis and recommendations are primarily habitat focused. Additional factors contributing to coho salmon viability (e.g., hatchery impacts, harvest impacts, and parasites) are beyond the focus of this analysis. The Plan provides a synthesis of available information in the basin. The Plan then provides an analysis and recommendations for the priority reaches in the watershed and priority types of actions to implement. Finally, the Plan provides an estimate of costs associated with implementation of the recommended restoration work. 2 OVERVIEW OF WATERSHED SETTING The Deschutes River watershed in Thurston County, Washington, encompasses approximately 166 square miles. The river originates on Cougar Mountain (3,870 feet) in the Snoqualmie National Forest and flows in a northwesterly directions for 57 miles. At river mile (RM) 2, the river flows over Tumwater Falls into Capitol Lake which was formed in 1951 by impounding the historic estuary of the river. Capitol Lake drains into Budd Inlet in South Puget Sound. The Deschutes River upstream of Capitol Lake is the focus of the analyses conducted for this plan (Figure 1, next page). Much of the upper watershed occurs in the transient snow zone between 1,100 and 3,600 feet elevation (Haring and Konovsky 1999). Transient snow zones are areas where rain-on-snow precipitation events are common. The lower 41 miles of drainage flow through a broad prairietype valley floor. Much of the middle-upper and upper watershed is managed for timber harvest by the Weyerhaeuser Company. The middle portion of the watershed also supports open farmland interspersed with dense stands of mixed deciduous and coniferous growth Page 1

8 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Figure 1. Vicinity Map (Haring and Konovsky 1999). The lower portion of the watershed is an urban growth management area where the river flows through the city of Olympia. 3 SYNTHESIS OF COHO SALMON UTILIZATION OF DESCHUTES RIVER WATERSHED 3.1 History of Salmon in Deschutes River In 1954, three years after the construction of Capitol Lake, a fish ladder was completed at Tumwater Falls. The fish ladder allowed anadromous salmonid populations past the natural barrier to utilize the Deschutes River and its tributaries. Another waterfall at RM 41, the Deschutes Falls, forms the upper extent of anadromous salmonid distribution in the river. Four species of salmon and trout occur in the Deschutes River watershed. Coho salmon (Oncorhynchus kisutch) are the most abundant anadromous salmonid. Chinook (O. tshawytscha), steelhead/rainbow trout (O. mykiss), and cutthroat trout (O. clarkii) also occur in the watershed. Chinook and steelhead returns are quite low, as adult chinook are hatchery-origin fish that are largely prevented from migrating past the fish ladder at RM 2. All coho and steelhead are allowed past the fish ladder for natural spawning in the river. Page 2

9 Number of Coho Adult Returns DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Given the presence of a natural barrier to passage at RM 2 prior to the construction of the fish ladder, coho salmon are not native to the Deschutes River. Hatchery-origin coho from around Puget Sound (primarily Green River stock) were planted in the river between the late 1940s and 1981 (WDF et al. 1993). Since 1981, there have been no coho releases into the Deschutes basin for production purposes. Due to the absence of hatchery releases, the coho stock in the Deschutes River is sustained by natural production and strays from other watersheds. Since 2012, there have been limited releases of hatchery coho fry in the upper watershed to support habitat utilization research. 3.2 Coho Salmon Population Trends WDFW has collected a long-term database of the number of coho salmon exiting the system as smolts and as adults returning to spawn. Smolt counts are monitored at a smolt trap operated below Tumwater Falls (RM 2, WDFW 2012). Counts of adult coho salmon returning to the river are made at the fish ladder at Tumwater Falls. As a result, WDFW has exceptional long-term data on fish out and fish back to the Deschutes River. Coho salmon returns to the Deschutes River have been quite low for approximately 25 years (approximately 8 full life cycles). Prior to 1988, WDFW reported adult coho returns often between 4,000 and 6,000 fish with numbers as high as 10,000 fish (Figure 2, WDFW unpubl. data). Only once since 1989 have the number of adult coho returns topped 3,000 fish. The result of this decline is that for two of the three coho cohorts (i.e., two years out of every three years), the number of returning adults is critically low (less than 200 fish). In fact, in one year (2002) the numbers dropped to only 28 returning adults to the watershed. A vast majority of wild coho salmon in Washington exhibit a 3-year life cycle (Weitkamp et al. 1995) such that there are three distinct brood year lineages (called cohorts or brood lines) with limited exchange between year classes (NMFS 2012). The strongest cohort, named cohort A for this analysis, has returned as adults most recently in years 2009 and 2012 and will produce adult returns again in 12,000 10,000 8,000 6,000 4,000 2,000 0 Adult Return Year Figure 2. Annual Number of Coho Adult Returns to the Deschutes River Since 1980 Page 3

10 Number of Adult Coho Returns Marine Survival Rate (preharvest) Number of Coho Adult Returns DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Although the numbers of adult returns are low, particularly for two of the cohorts the numbers have been generally stable within each cohort since 1997 (Figure 3). The reduction in adult coho returns coincided with a steep reduction in the marine survival rates (pre-harvest) observed among Deschutes River coho (WDFW unpubl. data, Figure 4). 2,500 2,000 1,500 1, Cohort A Cohort B Cohort C Adult Return Years Figure 3. Recent Coho Adult Returns for Each Cohort 12,000 10,000 8,000 6,000 4,000 2,000 Returning Adult Coho Pre-harvest Marine Survival Rate 0 0% Adult Return Year Figure 4. Annual Number of Coho Adult Returns and Marine Survival Rate in Deschutes River 35% 30% 25% 20% 15% 10% 5% 4 EVALUATION OF HABITAT CONDITIONS 4.1 Geomorphology of the Deschutes Basin Effective biological recovery requires a plan that works within the context of basin geomorphology. The Geomorphology of the Deschutes Basin includes the physical attributes of the basin as well as the physical processes that shape the landscape and drainage network. Page 4

11 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Previous studies (e.g. Chapman 1988) have shown that high levels of fine sediment, such as those documented in the Deschutes River and its tributaries, negatively affect salmon health. The following discussion focuses on the supply and transport of fine sediment in the Deschutes Basin drainage network, spatial variability, and the implications for the potential to improve conditions Overview The Deschutes Basin encompasses approximately 166 square miles in Western Washington draining portions of the Western Cascade Mountains and the Puget Sound Lowland. The Deschutes River flows approximately 57 miles from its headwaters in the mountains to its outlet passing through Capitol Lake and discharging to Budd Inlet in Olympia, Washington. Land use within the basin includes managed timber lands, agricultural lands, and residentially/commercially developed lands located within incorporated city boundaries for Olympia, Tumwater, and Lacey. Approximately 11 percent of the watershed is considered built environment (Thurston County 2011). Ground elevation within the basin ranges from sea level up to 3,870 ft in the headwaters. Topography varies widely ranging from flat and gently rolling hills up to steep valley sides and sharp ridges Geology Geology transitions at Deschutes Fall (approximately River Mile 41) from primarily Tertiary volcanic rocks in the headwaters to a combination of glacially derived material and alluvial floodplain deposits in the middle and lower basin. The glacially derived deposits occupying the majority of the river basin below RM 41 are composed of unconsolidated silt, sand, and gravel. Geologic variability in the headwaters leads to notable differences in landscape geomorphology and variable prevalence of landslides among the headwater tributaries. The upper basin ranges in elevation between 800 ft at Deschutes Falls up to and 3,870 ft with variable geologic conditions. The underlying geology of the upper basin is primarily Tertiary volcanic rocks of the Northcraft Formation with exposures of the sedimentary Skookumchuck Formation. Landslides are common within the upper basin tributaries, but the frequency and magnitude of landslides varies among the tributary basins based on differences in geology. Upstream of the West Fork confluence (RM 48) underlying geology is competent volcanic rock. Creek channels form V-shaped valleys with steep, straight slopes (Collins 1994). Tributary streams in this uppermost part of the basin include West Fork, Mine, Ware, and Hard creeks. Steep slopes and shallow soils generate relatively small surficial landslides, but the underlying hard rock generally remains intact and prevents the formation of deep-seated landslides (Thorsen and Othberg 1979). Between Deschutes Falls and the West Fork (RM 41 to RM 48) the primary geology is weathered volcanic rocks (Collins 1994; Thorsen and Othberg 1979). Lewis and Lincoln creeks are major tributaries in this reach. Page 5

12 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Downstream of Deschutes Falls for approximately 7 miles the valley width of the mainstem varies between alluvial floodplain wider than 500 ft and a narrow valley confined by high glacial outwash terraces (Collins 1994). Bank erosion in this reach mobilizes sediment derived from both glacial deposits and alluvial floodplain soils. Major tributaries in this reach include Fall, Mitchell, Huckleberry, Johnson, and Thurston creeks. Geology within the tributaries is predominantly weathered volcanic rock. Fall, Mitchell, and Huckleberry creeks are deeply incised with steep inner gorges that expose both weathered volcanic rock and sedimentary rocks from the Skookumchuck Formation (Thorsen and Othberg 1979). The lower reaches of Huckleberry and Mitchell creeks are less steep and formed in glacial sediments. Sediments delivered by landslides in the upper reaches of these drainages are episodically deposited in these reaches and reworked before being delivered to the mainstem. The landscape within the lower and middle basin is formed on glacially derived deposits including glacial terraces and outwash plains. Flat or gently rolling topography dominates, and the land is covered in forests and prairies. The Deschutes River has a well-developed floodplain composed of recent alluvial deposits formed on top of glacially derived deposits. Floodplain width varies from 400 4,000 ft with the edges of the valley bounded by high glacial terraces. Topography ranges from sea level at the mouth up to 500 ft elevation near Vail, Washington. Bank erosion within the lower and middle reaches mobilizes sediments derived from both glacial deposits and alluvial floodplain deposits Hydrology The Deschutes River Basin is approximately 166 square miles in area. Much of the upper watershed occurs in the transient snow zone between 1,100 and 3,600 feet elevation (Haring and Konovsky 1999). Transient snow zones are areas where rain-on-snow precipitation events are common. Rain-on-snow precipitation events have an effect limited primarily to the upper basin tributaries. Due to the relatively low elevation range for the majority of the basin area, hydrology is dominated by rainfall rather than snow melt or meltwater from glaciers. Spring and summer snowmelt is not a contributing factor to annual flow like other western Cascade basins. Peak flow events therefore occur primarily between October and March during the wettest time of year. Mean annual rainfall varies with elevation and generally ranges from 50 to 90 inches. Channel forming discharges and peak flow events result from rainfall runoff rather than from rain-on-snow events. Mean annual discharge is reported to be 396 cubic feet per second (cfs) by USGS at the Tumwater Gage (USGS Gage No ) based on 30 years of record. Maximum observed peak flow was 10,600 cfs on February 9, 1996, and minimum observed flow was 46 cfs on September 29, 2003 (USGS 2015) Sediment Supply and Transport Fine sediment sources derive from both natural and human-influenced processes. Natural processes including landslides, surface erosion, and stream bank erosion contribute fine sediments to the drainage network. Each of these mechanisms can be altered by human influence. Human-influenced sources of sediment include surface erosion of unpaved roads, landslides associated with roads and recent clear cuts, and accelerated bank erosion caused by Page 6

13 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN multiple factors (e.g., adjacent land use from agricultural and residential development, as well as secondary effects related to increased stream flow and sediment load). Two sediment supply studies were conducted that assessed sediment contributed by bank erosion and other sources (Collins 1994; Raines 2008). The Raines study compared bank erosion rates for the period 1991 through 2003 with earlier rates developed by Collins for the period 1981 through 1991 to estimate total average annual sediment yield from bank erosion. Average annual total sediment yield for the earlier period was estimated at 87,000 cy/year compared to 62,000 cy/year for the period For the earlier period, erosion of glacial terraces contributed the majority of sediment, while for the later period, erosion of floodplain deposits contributed more. The total contribution of sediments from bank erosion was used to calculate the net contribution of fine sediments from bank erosion. The result for the two periods differed more than the total load due to differences in sources. Net contribution of fine sediments from bank erosion was 28,000 cubic yards/year (cy/year) for the period compared to 4,900 cy/year for the period Surface erosion from unpaved roads was estimated to be 5,901 cy/year (Raines 2008). The Collins (1994) report included an assessment of contributions attributable to landslides based on an inventory that was current at the time of the study. The TMDL Technical Report (Ecology 2012) provides an overall sediment budget including both fine sediments and coarse sediments (gravel) partitioned according to sources. The draft TMDL report (Ecology 2015) utilized previous work by Raines and Collins to summarize sources fine sediment loading and divide the total load into portions attributable to human sources, natural sources, and unaccounted sources. Unaccounted sources were estimated based on comparison to the long-term average loading to Capitol Lake. The average annual total load of fine sediments is estimated to be 27,315 cy/year including Natural Sources (13,800 cy/year), human sources (5,700 cy/year), and unaccounted sources (7,815 cy/year). The TMDL sets a goal of eliminating the human sources of fine sediment. The amount of sediment in active transport within the river bed varies over time as sediment inputs are generally episodic in nature, and sediment transport varies episodically with high flow conditions. Sediment derived from bank erosion of alluvial floodplain deposits does not result in a significant long-term net input of sediment to the system since such sediments are temporarily mobilized deposited again as part of meander migration and overbank sediment deposition on the floodplain. The short term amount of fine sediment in the river bed is affected by the amount and intensity of bank erosion even if the net input of sediment is reduced Geomorphic Implications for Biological Recovery The TMDL goals for fine sediments address average annual inputs, but sediment inputs are episodic in nature, and short-term loading rates can be an order of magnitude greater than the annual average. The process of routing sediment through the river in response to large sediment inputs can take years or decades. Bank erosion along the mainstem Deschutes River results in the largest contribution of fine sediments to the system. The intensity and amount of bank erosion directly affects the amount of fine sediment in the riverbed. The total sediment contribution (not just net contribution) affects the short-term bed composition since reworked Page 7

14 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN sediments are in transport between erosion and deposition sites. Ongoing bank erosion would likely maintain high concentrations of fine sediment in the river bed even if the net contribution of fine sediment is reduced according to the goals of the TMDL due to the temporal effects of sediment inputs and river response. Response time for tributaries is much faster in comparison to the mainstem river due to the steeper gradient, particularly in the upper watershed, and shorter reach lengths. Stabilizing and reducing sediment inputs combined with restoring instream habitat conditions in the headwater tributaries downstream of the anadromous fish passage barrier at Deschutes Falls can be accomplished in a shorter time and with a smaller and more focused effort compared to addressing bank erosion inputs on 40 miles of the mainstem Deschutes. The total fine sediment load includes human-influenced sources, natural sources, and unaccounted sources. The human-influenced sources of fine sediment are only about 20 percent of the total. The natural sources will continue to contribute a large amount of fine sediment to the system. Any biological recovery plan must consider and account for the ongoing presence of fine sediment. As noted above, the mainstem channel response time to fine sediment inputs is much longer than tributary response time, particularly in the upper watershed tributaries with steeper gradients. Restoration efforts in the tributaries can be expected to produce faster results in support of biological recovery. Same year recovery for portions of the streambed can be accomplished by increasing the complexity of instream structure using large wood. Hydraulic diversity enhances sorting of sediments. Sediment sorting can produce pockets of relatively clean gravel even in a system enriched with fine sediments. Reducing fine sediments in the mainstem Deschutes River can only be achieved as a long-term objective due to longer river response time to sediment inputs, and the short-term effects of ubiquitous bank erosion. Higher priority should be given to stabilizing and improving conditions in and above coho spawning areas, notably the upper watershed tributaries and upper mainstem areas (i.e., RM 31-41). This recommendation includes sediment inputs from sources upstream of the anadromous zone because those areas also affect these downstream areas. Secondarily, long-term efforts can be directed toward addressing sediment inputs in lower watershed tributaries and along the remainder of the mainstem. 4.2 Salmon Habitat Limiting Factors The most recent habitat surveys in the Deschutes River were conducted in the 1990 s and early 2000 s. Cramer (1997) and ATEC (2001) combined to collect habitat data in 343 mainstem reaches spanning the 40 miles between the Deschutes Falls at the upper end of the anadromous zone and Tumwater Falls (RM 2). The study provided instream and riparian habitat data in mainstem reaches that averaged just over 600 feet in length. The Squaxin Island Tribe inventoried habitat in representative reaches distributed along the mainstem in Schuett-Hames and Flores (2004) and Schuett-Hames and Child (1996). The Squaxin Island Tribe inventoried the distribution of off-channel habitats along the entire mainstem in 1999 (Taylor 1999). Tributary habitats in the upper watershed were surveyed in two studies by the Squaxin Island Page 8

15 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Tribe (Schuett-Hames et al. 1991) and (Schuett-Hames and Flores 1994). Habitat data were collected in Spurgeon Creek (flows into mainstem on right bank at RM 10) in 2006 (Steltzner and Haque 2006). Based on the available habitat data for salmonids, a Habitat Limiting Factors report was prepared for the Deschutes River and independent tributaries in WRIA 13 Haring and Konovsky (1999). The Habitat Limiting Factors are still considered applicable for the watershed and are summarized below Fish Passage Beginning at the mouth of the Deschutes, access to the river by returning adult salmon from Budd Inlet is restricted by dam (and tide gate) under 5th Avenue in Olympia, which forms Capitol Lake. Salmon can pass the tide gate when open, and through a constructed fish ladder. However, the fish ladder can present a barrier during certain tidal elevations and when there is insufficient surface water elevation in Capitol Lake to provide 6 inches of flow over the top step in the ladder, which can lead to a migration delay and potential for increased predation during this delay below the tide gate (Haring and Konovsky 1999). Culverts and other passage barriers along many of the tributaries in the middle and lower portions of the river restrict salmon access. The passage barriers in this portion of the basin are more restrictive of juvenile coho accessing rearing and overwintering habitats than they are for adult coho accessing spawning habitats (Haring and Konovsky 1999) Substrate Past studies have documented that most of the coho spawning in the system occurs in the upper mainstem and tributaries (Sullivan et al. 1987). This is despite the fact that Schuett-Hames and Flores (1994, cited in Haring and Konovsky 1999) reported that spawning conditions are generally not good above Vail due to elevated levels of fine sediment (<0.85 mm diameter). Of the eleven reaches measured, three (two in tributaries and one in mainstem) were rated as good (<12% fines), six (two in tributaries and four in mainstem) were rated as fair (12-17% fines), and two (one in each tributary and mainstem) were rated as poor (>17% fines). Schuett-Hames and Child (1996) reported that the mainstem of the Deschutes has also been found to lack good spawning conditions due to fine sediment levels, with four reaches evaluated rating as poor, and only one as fair. Forest roads and culverts have been thought to be a primary contributing factor to elevated fine sediment loads in the upper Deschutes watershed (Sullivan et al. 1987). Bilby (1985, cited in Sullivan et al. 1987) reported that a single culvert in the Johnson Creek basin draining a high proportion of the road network directly to the stream, contributed 21% of the annual sediment load of the sub-basin. Road densities ranged from 2.4 to 4.7 km/km 2 in the upper Deschutes basin based on a road network inventory in 1986 (Sullivan et al. 1987). Landslides and debris flows are also a significant factor in fine sediment loading. Sullivan et al. reported seven major mass failures over a 12-year monitoring period. Toth (1991) evaluated 76 Page 9

16 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN road damage sites in the upper watershed following the January, 1990 floods and found 25 of 38 landslides evaluated to be associated with roads. The Squaxin Island Tribe (1991, cited in Haring and Konovsky 1999) identified that the Huckleberry Creek channel upstream of the 1990 landslides had approximately a 1:1 pool to riffle ratio, while cascades dominated the area below. The channel below the debris flow was reported to be aggrading. They reported 16% fines (fair) in the substrate above the debris flow, and 20% (poor) in the substrate below the debris flow. Moore and Anderson (1979, cited in Haring and Konovsky 1999) found that Mitchell Creek transported the greatest amount of sediment of the tributaries in the upper watershed, contributing approximately 19% of the total load of the river above the Weyerhaeuser 1000 Road. The Deschutes is also considered a geologically young watershed, and is thought to have an inherent amount of fine sediment entering the system from normal geologic processes, particularly through erosion of glacial terraces (Raines 2005). Collins (1994) reported that the majority (80%) of eroded material at 127 erosion sites from were sand-grained size or smaller Streambank Stability Streambank stability and bank erosion are significant geomorphic factors to habitat formation as they strongly influence channel morphology and substrate composition. Bank erosion contributes to channel instability, substrate aggradation and scour, and increased fine sediment levels in the channel substrate (Haring and Konovsky 1999). Cramer (1997) documented extensive active bank erosion along both banks of the mainstem. Collins (1994) and Cramer (1997) indicate that because the Deschutes is a geologically young watershed, channel erosion would be common whether mature riparian vegetation was present or not. In this situation, geologically young means that the process of recent valley formation and landscape evolution has been going on only since about 12,000 years before present at the end of the most recent glaciation. Collins (1994) concluded that the dominant influences on the rates and locations of eroding banks are geologic and topographic. Adding support to this finding, Cramer (1997) did not find a strong correlation between human modification and significant bank erosion, although field observation indicated a high occurrence of erosion downstream of armored banks and pastures where riparian vegetation had been cleared. Natural bank erosion along the mainstem is thought to be the primary contributor of both fine and coarse sediment to the river below Deschutes Falls (Collins 1994). Bank erosion and landslides are a particular concern in the upper tributaries managed for timber harvest. The removal of vegetation on hillsides has contributed to substantial inputs of fine sediment to the tributaries and river. This limiting factor indicates the importance of maintaining mature riparian vegetation along a wide buffer of the tributaries and on unstable slopes. Page 10

17 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Large Woody Debris Large woody debris (LWD) is an important habitat-forming factor in Pacific Northwest streams (Bisson, et al. 1987). Haring and Konovsky (1999) report similar findings from Schuett-Hames and Child (1996) and Cramer (1997) that LWD abundance in measured reaches of the mainstem Deschutes rated primarily as good to fair (>1 piece per bankfull width). However both studies noted a predominance of small to medium sized LWD and a lack of large, key piece LWD. The smaller wood pieces are considered less stable and not as effective as forming habitat as larger pieces. Haring and Konovsky (1999) report a deficiency of key pieces of LWD. The combined dimensions described by Bilby (1985) and Cramer (1987) for wood to be a key piece for a river the size of the Deschutes are inches diameter and feet in length. The removal of mature forest and alteration of riparian buffers significantly limits the potential for near-term recruitment of LWD, significantly limiting habitat forming potential for salmonids in the Deschutes basin Pool Habitat Pools provide important slow water habitat for rearing juveniles and cover and resting habitat for spawning adults. Pool tailouts tend to provide good substrate, depths, and velocities to support salmon spawning. The mainstem Deschutes is thought to have generally sub-optimal pool habitat conditions. Cramer (1997) reported that forty seven percent of reaches had >4 bankfull widths per pool (poor), 29% of the reaches had 2-4 bankfull widths per pool (fair), and 24% of the reaches had <2 bankfull widths per pool (good). Further, Haring and Konovsky (1999) suggest that much of the habitat identified as pools does not function as true pool habitat creating habitat complexity and beneficial pool:riffle sequences. Instead, much of the mainstem pool habitat is more like long complex runs with adequate depth to qualify as pool habitat. The lack of quality pool habitat is consistent with the lack of LWD, particularly key pieces, described above Off-Channel Habitat Off-channel habitat in the mainstem is considered less prevalent than historical conditions (Haring and Konovsky 1999). Cramer (1997) found that only 11% of the 343 reaches had high availability of off-channel habitat and only 17% more had medium availability. Additional offchannel habitat is identified as essential due to its benefits to coho salmon as stable habitat for rearing, spawning, and refuge during high flow events Riparian Vegetation Buffers Riparian buffers provide several critical functions to healthy stream habitat including inputs of LWD and other organic material, shade, streambank stability, and the potential to improve water quality. Haring and Konovsky (1999) report that riparian buffers have been highly altered throughout the Deschutes basin from forestry practices, agricultural uses, and urban / suburban development. Page 11

18 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Cramer (1997, as cited in Haring and Konovsky 1999) reported that only 2% of the left bank area, 5% of the right bank area, and 1% of both banks had estimated riparian widths >30 meters with the sampled reaches (38 river miles). The majority of the sampled reaches had riparian buffers <10 meters wide. Additionally, trees identified in the sampled riparian zones were primarily deciduous. Limited riparian buffer area and lack of coniferous species is also consistent with the lack of key piece LWD. As described above, mature vegetation is needed along riparian buffers and on unstable slopes to reduce the occurrence of landslides and bank erosion Water Quality Haring and Konovsky (1999) note that the Deschutes is on the 303(d) list for several water quality parameters. Capitol Lake, at the mouth of the Deschutes, was noted to be on the 303(d) list for high fecal coliform bacteria and high total phosphorus. They report that other water quality concerns had been identified for Capitol Lake including low dissolved oxygen and high temperature. The mainstem of the Deschutes was noted to be on the 303(d) list for high fecal coliform, high temperature, and ph. Consistent with the findings related to sediment and erosion, they also report that the Deschutes carries a very high fine suspended sediment load during peak flows. Sullivan et al. (1987) reported that water temperature had increased significantly in two small headwater streams with timber harvest from 1974 to Washington Department of Ecology is currently leading an effort to develop a Total Maximum Daily Load (TMDL) for the Deschutes Basin addressing multiple water quality parameters including temperature, fine sediment, and bacteria (Ecology 2012; Ecology 2015). The implementation plan for the TMDL includes actions that are directly relevant to biological recovery within the basin Water Quantity The hydrologic regime of the Deschutes basin is a significant factor for habitat quality for salmonids. The basin has only moderate to low elevation, lacks winter snowpack, and runoff is dominated by rainfall (Collins 1994). Peak flows are typically seen in the late fall and winter. Spring and summer snowmelt is not a contributing factor to annual flow like other western Cascade basins, and summer low flow conditions have been identified as a concern for coho salmon (Haring and Konovsky 1999). Haring and Konovsky (1999) report that the Deschutes is on the 303(d) list for instream flow concerns. Minimum instream flow levels have been established for the Deschutes pursuant to WAC Page 12

19 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Estuarine Estuaries are very important habitats for salmonids that have naturally adapted to conditions that provide a brackish or lower salinity transition zone between fresh and salt water. Relative to other salmon, coho are moderately dependent on estuaries for rearing (Healey 1982). The creation of Capitol Lake has effectively eliminated the natural estuarine conditions at the mouth of the Deschutes, which would have historically extended upstream to Tumwater Falls (Haring and Konovsky 1999). The presence of Capitol Lake has created an abrupt transition from fresh water to the marine waters of Budd Inlet. Salmonids negotiating this abrupt entry to the marine environment lack the gradual transition between salt and fresh water that they are adapted to. Haring and Konovsky (1999) also describe an apparent affinity for all salmon species to forage on benthic prey items in the upper estuary habitats of their natal rivers; however, those habitats are currently not available to salmon in the Deschutes River watershed. 4.3 Habitat Deficiencies By Life Stage A lack of quantitative habitat data available since the 1999 Limiting Factors report leaves us with significant data gaps for current habitat conditions and limiting factors. Using the previously identified habitat limiting factors in the Deschutes basin, the following section synthesizes limiting factors in the context of coho salmon life history stages. Life history traits are directly related to survival and reproduction, and an inherent expression of a species interaction with its environment. The below sections address the key habitat deficiencies in the watershed relative to our understanding of the life history strategies of Deschutes River coho salmon and their habitat utilization Adult Migration and Spawning Adult coho move through the entire anadromous zone of the Deschutes River en route to available spawning areas 1. Most coho salmon spawning occurs in the tributaries between RM 31 and RM 41. The WDFW spawning ground database dating back to 1980 includes varied levels of effort at mainstem and tributary sites; however, among those years that included mainstem observations, between 94 to 98 percent of the adult coho were observed in the upper watershed tributaries. Huckleberry Creek at RM 38.2, Johnson Creek at RM 39.1, and Thurston Creek at RM 39.4 have historically supported the largest portion of the spawning fish based on WDFW spawning surveys (WDFW 2015). Of these, Huckleberry Creek has supported the largest number of spawning coho although the creek is continuing to recover from massive landslides and debris flows in January Mitchell Creek at RM 38.1, Fall Creek at RM 35.3, and Pipeline Creek at RM 31 also support coho spawning. Spawning also occurs in the mainstem above RM 31 (WDFW 2002, cited in Anchor 2008) with most occurring upstream of 1000 Road (approximately RM 35, Sullivan et al. 1997). WDFW (2015) documents spawning in Spurgeon 1 The term upper watershed is applied throughout this document to refer to the upstream portions of the watershed that are accessible to anadromous fish (i.e., downstream of the Deschutes Falls at RM 42 to RM 31). The true upper watershed is the river and tributary habitats located upstream of the natural barrier. Page 13

20 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Creek and small areas in the lowermost reaches of a limited number of other middle and lower tributaries are shown as supporting spawning (WDFW 2002, cited in Anchor 2008). The habitat limiting factors affecting adult migration and spawning are: Fish passage Mainstem habitat complexity, particularly pools with structure for cover and off-channel habitats Spawning ground habitat complexity, particularly pools with structure for cover and suitable substrate At the point of entering the river, fish passage is restricted by Capitol Lake. This occurs through the concentration of adult coho to pass through the limited opening provided by the tide gate and fish ladder at the dam which makes the fish vulnerable to marine predators such as seals. During upstream migration, suitable habitat conditions are needed. Adult coho typically begin to enter the river in the fall when water temperatures decrease and flows increase. As adult coho salmon migrate upstream they use the main channel of mainstem rivers and tributaries for migrating to spawning sites. They utilize all habitat types within the main channel and can generally be found holding to rest during the migration in deep water areas, particularly pools. The lack of habitat complexity in the mainstem of the Deschutes is evidenced by the lack of pools, the paucity of LWD, and the limited extents of sufficiently wide riparian buffers of mature vegetation. As reported by Haring and Konovsky (1999), the mainstem pools reported by Cramer (1997) are of insufficient quantities, and considered an overestimate of pool habitats because they function more like run habitats. The LWD that is available in the mainstem has very few of the large key pieces that can provide long-term stability and pool habitat formation. Coho salmon spawn primarily in the upper tributaries between RM Some coho spawning has been documented in the mainstem, but the numbers tend to be low (WDFW 2015). The amount of coho spawning in the mainstem could be due to poor habitat conditions. It could also be related to the overall low numbers of spawners in the watershed and the mainstem habitats would be utilized more if there was more competition for space in the upper tributaries. Coho typically spawn in pool tailouts and along the margins of riffles. They generally spawn in small gravels and in close proximity to cover. The important pool tailout habitat used for spawning signifies the need for LWD, particularly key pieces, to form the habitat and provide cover habitat. Riparian vegetation improves spawning habitat by providing overhanging vegetation for cover, root mass to maintain banks and allow formation of undercut banks in some locations, and long-term LWD recruitment into the tributaries and mainstem. Coho also spawn heavily in small groundwater-fed tributary channels where these habitats exist along the floodplains of rivers, often in relatively high densities (Lestelle 2007). Groundwater channels often have fine substrates with high amounts of fine or sand sized particles. These areas, despite their high concentration of fine sediment, can produce high egg survival because of upwelling that occurs there (Bjornn and Reiser 1991). Taylor (1999) indicates Page 14

21 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN limited off-channel habitats upstream of RM 29. To the extent that quality pools and groundwater channels are lacking along the mainstem and tributaries where spawning generally occurs, this may be limiting on coho production Incubation and Emergence Coho egg incubation and emergence from the gravel as alevins occurs in very close proximity to where spawning occurred. Incubation and emergence occurs generally through the winter and early spring, and depends on spawn timing and incubation temperature (Sandercock 1991). The habitat limiting factors affecting incubation and emergence include: Fine sediment Peak flows and scour Successful egg incubation and alevin development is highly dependent on clean, well oxygenated gravel. Factors including fine sediment deposition and scour are widely considered to affect survival to emergence of salmon fry (Bjornn and Reiser 1991). Survival to emergence in the Deschutes basin is likely variable among the local stream conditions. Fine sediments that embed the redd during incubation affect the dynamics of water interchange, oxygen availability, metabolic waste dispersal, and the movement of alevins. Tagart (1984, cited in Lestelle 2007) reported that relatively small increases in fine sediment produced a steep decline in survival. Fine sediment loading due to forest management practices and debris slides in the tributary reaches of the Deschutes have been well documented (Sullivan et al. 1997, Toth 1991). Toth (1991) noted a strong correlation between roads and sediment delivery to streams from landslides and Bilby et al. (1989) noted a direct relationship of forest road use and increased sediment delivery to the drainage network. Given the amount of fine sediments reported in Haring and Konovsky (1999) for the tributary reaches, this factor should be considered limiting on survivability from egg to emergence where fines exceed 12%. Peak flows and resulting bed scour are known to potentially have significantly adverse effects to incubating salmon eggs. Increased rates of bed scour have been attributed to lack of stable LWD and increased peak flows from timber harvest and road building (Montgomery 1996, cited in Lestelle 2007), which is prevalent in the tributary reaches of the Deschutes basin. Lamarche and Lettenmaier (1998) reported that combined effects of forest harvest and roads increased the simulated peak flows for the 10-year return flood in the upper Deschutes basin by roughly 15%, and roads alone accounted for an increase of 2% to 10% in the mean annual flood (~2.3 year return interval) in the modelled sub-basins. They suggest that placement of drainage structures that reduce the road connectivity to the stream network can mitigate the effects of increased flows. Visual observation of the upper watershed on commercial timberland reveals that both road density and lack of forest cover due to timber harvest is still quite high. Peak runoff events and sediment loading are likely limiting on incubation and emergence success in the spawning Page 15

22 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN reaches. These factors indicate the need to continue to evaluate the source control of runoff patterns and fine sediment delivery to the upper watershed reaches influenced by managed forestland. Vegetation management, particularly riparian zones and areas affected by road drainage, can moderate peak plows and mitigate the effects of fine sediment delivery by trapping sediment and providing long-term hydraulic benefits from LWD inputs. Stable LWD can promote beneficial sorting of transported sediments and provide protection from high velocities in exposed areas during high flow conditions Spring and Summer Rearing Once fry emerge from the gravel, they will begin to disperse to suitable spring and summer rearing habitat. Coho rearing in the Deschutes is thought to occur primarily in the natal tributaries, but individuals are likely to make use of available preferred habitat based on competition and availability. Coho fry typically exhibit territorial behavior and will distribute throughout the stream, establish territories, and remain for extended periods of time (Hoar 1958, cited in Sandercock 1991). The habitat limiting factors affecting coho rearing include: Habitat complexity, particularly low velocity habitats (i.e. pools) in association with LWD and riparian cover Low summer flows and elevated temperature Off-channel habitat, particularly groundwater channels that provide thermal refuge Fish passage; culverts and other obstructions that inhibit movement into middle to lower tributaries and/or off-channel habitat Fine sediment load This appears to be a critical life history stage for coho salmon in the Deschutes basin with respect to being affected by multiple previously identified habitat limiting factors, including LWD abundance, pools, off-channel habitats, and summer low flows and temperature. Once emerged from the gravel, coho fry tend to disperse in search of low velocity habitats (Beecher 2002, cited in Lestelle 2007). In streams lacking suitable velocity refugia, fry survival is likely reduced if emergence occurs during periods of prolonged high flow (Lestelle 2007). Fish that emerge during high flows can be swept downstream, potentially to areas with less suitable rearing habitat. Coho parr are typically found in highest densities within their natal streams because most fry usually do not migrate long distances from spawning sites (Lindsay 1974, cited in Lestelle 2007). The headwater tributaries of the Deschutes have historically been considered important rearing habitat (Sullivan et al. 1987). Fransen et al. (1993) indicates that depth and current velocity are strongly correlated with coho rearing in Huckleberry Creek. They found that stable LWD that promotes scour pool formation was strongly correlated with influencing the preferred depth and velocity conditions. Roni and Quinn (2001, cited in Lestelle 2007) have reported that juvenile coho densities in smaller streams during summer are positively correlated with Page 16

23 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN quantity of large woody debris and that increasing amounts of large wood often yields more frequent and larger pools, which may result in greater numbers of juvenile coho per channel length. Debris torrents in Deschutes tributaries have had the effect of burying pool habitat and resulting in predominance of riffle habitat (Sullivan et al. 1997). Sediment loading from forest roads also has potential to diminish pool habitat. Fine sediments in suspension have been shown to result in effects such as gill abrasion and reduced feeding efficiency (Bash et al. 2001). The effects of sedimentation and the reduction of preferred habitat can be offset somewhat through stable LWD, which is dependent on functional riparian zone for long-term recruitment. The lack of mature forested riparian zones and associated long-term LWD recruitment potential likely also limits the potential for creation of preferred rearing habitat. A lack of low velocity habitat in the tributary reaches of the Deschutes, either due to channel simplification from sediment loading, or lack of LWD, is likely limiting on coho fry dispersal and available rearing habitat. Competition for limited rearing habitat and limited food can result in reduced growth at higher juvenile abundance (Fransen et al. 1993). Thus, the amount of suitable summer rearing habitat can limit coho production in a watershed. High water temperatures during summer can be an important factor affecting the distribution, growth, and survival of juvenile coho salmon (Carter 2005). Temperature affects metabolism, behavior, and survival of both juvenile fish as well as other aquatic organisms that may be food sources. The Deschutes River Total Maximum Daily Load (TMDL) Technical Report (Ecology 2012) simulated heat budget and water temperatures under various scenarios. The modelling indicates that under existing conditions, peak temperatures throughout the entire system would exceed 16 C and that many areas would exceed the lethality threshold of 22 C. The highest temperatures modelled in the Deschutes occurred between RM 26 and RM 34, which almost certainly limits rearing potential along this section of the mainstem. Potential sources of temperature impairments in streams identified in Roberts et al. (2012) include low summer streamflows due to natural conditions and anthropogenic activities, elevated temperatures from stormwater runoff, increased stream surface area due to natural and anthropogenic activities, and the lack of riparian shade. The Deschutes River is highly dependent on groundwater discharge during the dry summer months. Municipal, industrial, and agricultural uses all put high demand on groundwater. Future TMDL implementation strategies should stress the need to maintain groundwater baseflows in these streams, particularly during the summer when elevated stream temperatures are most detrimental to salmonids and native trout (Ecology 2007). Agricultural surface diversions have the greatest influence on stream flow in summer when need is high and stream is naturally low (Pacific Groundwater Group 1995). Because temperature and flow volume are inversely related (Poole and Berman 2001), minimizing groundwater withdrawals and maintaining summer baseflows are recommended to mitigate the effects of elevated temperature (Roberts et al. 2012). Page 17

24 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Based on their simulation, Roberts et al. (2012) indicates that establishing the system-wide potential from mature riparian vegetation and riparian microclimate can reduce peak temperatures by an average of 4.5 C throughout the Deschutes River. Sullivan et al. (1997) reported that the 7-day maximum water temperature had increased as much as 8.9 C in headwater streams following timber harvest and shade reduction, supporting the importance of shade on headwater streams. The location of the highest modelled temperatures occurs just downstream of the majority of the tributary inputs to the mainstem (RM 34 to RM 41), which suggests that the tributaries may not be providing significant cooling effects. Mature riparian zones along headwater streams would promote benefits of shade and microclimate effects on temperature in core rearing areas. Mature riparian zones can have secondary benefits on temperature through LWD inputs and associated pool formation. Watershed Sciences (2004) noted a 1 C decrease in temperatures in the mainstem of the Deschutes River during the TIR survey through a logjam and attributed it to enhanced hyporheic exchanges. This again underscores the importance of LWD to habitat function in the Deschutes basin, where it is currently limited. One strategy that juvenile coho can employ to cope with high temperatures is to find thermal refuge sites, such as deep pools and groundwater channels. Nielsen (1992, cited in Lestelle 2007) reported that juvenile coho used cool water pools at confluences with cool tributaries and coldwater seeps along hillslopes where some groundwater influence exists. The importance of side channels and groundwater channels to summer rearing coho are described in several studies in Washington (Sedell et al. 1984; Rot 2003; Pess et al. 2005, cited in Lestelle 2007). These channels, in addition to providing thermal refugia, also provide the preferred low velocity rearing habitat. Groundwater channels normally have cooler water temperatures in summer than occur in mainstem rivers and their side channels. Taylor (1999) indicates limited off-channel habitats upstream of RM 29. A lack of these groundwater channels along the mainstem in the tributary reaches where summer rearing may occur, may be considered limiting on coho production Overwintering Juvenile coho typically move from their summer rearing locations in fall, triggered by increased flows associated with autumn rainfall (Sandercock 1991). Increased fall flows in the upper Deschutes, particularly in tributary rearing areas, likely cues movement downstream to the middle and lower reaches in search of low velocity off-channel areas, beaver ponds, low gradient tributaries, and other low velocity habitats. A winter survey of the Deschutes found coho to be most abundant in low gradient, spring-fed tributaries in the middle and lower basin, and along the margins of swamps (Thut et al. 1985, cited in Taylor 1999). The habitat limiting factors affecting coho overwintering include: Off-channel habitat, overflow and groundwater channels that provide high flow refuge Page 18

25 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Habitat complexity, particularly low velocity habitats (i.e. pools, alcoves, and tributary mouths) in association with LWD Fish passage; culverts and other obstructions that inhibit movement into middle to lower tributaries and/or off-channel habitat Increased peak flows Movement into low velocity overwintering habitats is another example of the species preference for slow-moving water. Low gradient tributaries and off-channel habitats provide refuge from high flow velocities that occur over the fall and winter months. Smolts coming from off-channel ponds are consistently larger than fish that overwinter and emigrate from runoff tributaries and small groundwater channels (Lestelle and Curtwright 1988). Overwinter survival in off-channel habitats has been found to be improved if cover in the form of wood is added (Giannico and Hinch 2003, cited in Lestelle 2007). The importance of large wood to overwintering coho salmon has also been documented by Cederholm et al. (1997, cited in Lestelle 2007). Nickelson et al. (1992, cited in Lestelle 2007) reported that juvenile coho predominantly overwinter in pools and alcoves in some streams, all having low velocities. These findings continue to support the importance of low velocity habitat and the contribution that LWD has in the formation of that habitat and as cover. Peak main channel flows with high velocities can force fish downstream into potentially less suitable habitats. LWD can play an important role in creating quiescent areas in main channel pools during winter storm events that can increase pool flow velocities. The results of Cramer (1997) and Taylor (1999) indicate that potential off-channel habitat is limited for the majority of the mainstem Deschutes. Low gradient tributary streams that may potentially provide overwintering refugia are infrequent along the mainstem Deschutes. Lack of key piece LWD and generally low pool quality in the mainstem Deschutes also limits the potential for overwintering refugia. The combination of these factors suggests that a lack of quality overwintering habitats along the mainstem Deschutes are likely limiting on the success and production of coho Smoltification Smoltification begins with migration from their overwintering habitat downstream toward the marine environment, thought to be cued largely by factors including flow, day length, and water temperature (Sandercock 1991). Smolts in the Deschutes basin migrate from overwintering habitats into the mainstem, downstream to Capitol Lake below Tumwater Falls, and ultimately out of Capitol Lake and into Budd Inlet. The habitat limiting factors affecting coho overwintering include: Habitat complexity, particularly low velocity habitats (i.e. pools, alcoves, and tributary mouths) in association with LWD Lack of brackish estuary; abrupt osmoregulatory transition Potential for predation Page 19

26 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Fish passage Smolt migration in the mainstem is again influenced by LWD and low velocity areas. McMahon and Holtby (1992, cited in Lestelle 2007) reported use low velocity areas under cover with occasional forays to the edge of cover to feed on invertebrate drift and the most often used cover type was large woody debris associated with pools. This suggests the importance of continuing to forage and use instream cover during periods of rest. They also indicate that shelter from high flow velocities is likely important to prevent premature displacement. Pools and low velocity areas with woody cover are important to this life stage also, and lack of such habitats can be limiting on coho fitness and survival. During outmigration, estuarine habitat provides an important role for salmonids transition from fresh to salt water. Among salmon species, coho exhibit an intermediate dependence on estuaries, with Chinook and chum being more dependent and sockeye and pink less dependent (Healey 1982). Recent acoustic tagging of wild coho from other South Puget Sound tributaries, Goldsborough Creek and Mill Creek in Hammersley Inlet/Oakland Bay, indicates some coho remain in the estuary for several days (Steltzner pers. comm.). Although sample sizes were limited, the majority of tagged wild coho outmigrating from Goldsborough Creek were detected in the estuary for at least 5 days and some of the fish were still in the estuary after 14 days. Estuarine rearing provides opportunities for continued feeding and growth priority to entry to the marine environment and to complete osmoregulatory transition from fresh to salt water. Neher et al. (2013) observed significantly better growth and body condition in coho that exhibited estuary rearing than those that did not. Estuaries are often highly productive areas that provide abundant prey items to support rapid growth. Estuaries also provide a gradual transition from fresh to salt water that Simenstad et al. (1982) suggests is likely beneficial given the physiological demands necessary for the juvenile fish to transform from survival in a freshwater environment to a saline environment. For salmon that enter the marine environment as smolts after rearing for a year or more in the freshwater environment, such as coho, salinity is also thought to cue this physiological transition (McCormick 1994). The detrimental effects of such abrupt transitions as occurs for fish exiting Capitol Lake have been hypothesized previously, but have not be researched. Other researchers have suggested that abrupt estuary transitions may result in delayed saltwater mortality. The abrupt transition from fresh to salt water at the mouth of Capitol Lake may also expose fish to an abrupt change in water temperature, as the lake temperatures are warmer than Budd Inlet temperatures, particularly later during the outmigration period. The effect of this change is unknown, but has been hypothesized as having an effect on fish outmigrating from the Lake Washington system which also has an artificially abrupt estuarine zone (SPU and USACE 2008). Moser et al. (1991) suggested the importance of estuary residence for orienting for return migration, in addition to osmoregulatory transition. Though Capitol Lake may offer some Page 20

27 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN additional rearing potential, the abrupt transition from fresh to salt water likely results in suboptimal conditions for osmoregulatory transition and orientation. In addition to the physiological stresses, survival through Capitol Lake is also affected by predation. Hayes et al. (2008) report that both largemouth bass (Micropterus salmoides) and smallmouth bass (M. dolomieu) may have a significant presence in Capitol Lake. Both these species are voracious piscivores, and are known to prey upon juvenile salmonids in lake environments (Tabor et al. 2006). If present, Northern pikeminnow (Ptychocheilus oregonensis) and cutthroat trout (O. clarkii) also may pose a predation risk to juvenile salmonids. Though no data were reported on these potential predator-prey interactions, it is reasonable to expect that some degree of predation on juvenile coho occurs during their residence in Capitol Lake, directly reducing their survival rate. It is reasonable to expect that estuarine rearing may benefit coho in this system, particularly if limited freshwater rearing and overwintering habitat have resulted in sub-optimal fitness of smolts upon their emigration to the marine environment. Therefore the lack of a brackish estuary environment is likely limiting on coho fitness upon their entry into the marine environment. 5 RECOVERY STRATEGY 5.1 Identification of a Recovery Goal for Coho Salmon The identification of a recovery goal for coho salmon in the Deschutes River focused on the population abundance (i.e., number of adult spawners) estimated to be sufficiently large enough to be resilient to environmental variation and human modifications. Sullivan et al. (1987) reported that a 1975 study by the Washington Department of Fisheries (WDF, now WDFW) estimated that the Deschutes provides enough suitable spawning habitat to support 7,600 coho. More recently, WDFW identified a population goal for the Deschutes as an escapement of 8,100 adult coho (WDFW 2011). WDFW (2011) notes 4,000 adults as an alternate number to use, but the source does not provide background on the basis for either number. A population simulation model called Shiraz was also used as an analysis tool to examine the population size necessary to maintain a resilient coho population. Shiraz is a Microsoft Excel based model which uses information on user-defined parameters characterizing habitat quantity and quality at each freshwater life stage (e.g., spawning adults, eggs, rearing fry, etc.). A Shiraz model for coho in the Deschutes River was developed in 2008 (Anchor 2008). This model was updated and refined for this analysis. The updated methods of the model are provided in Appendix A. Model inputs on habitat quality were adjusted (habitat quality was improved) to identify the population size at which the number of adult returns are stable over time (i.e., productivity = 1.0 and recruit per spawner ratio of 1:1) with the analysis period extending from 2015 to This analysis indicated that the strongest cohort, cohort A, stabilizes at approximately 3,500 adult coho. This analysis was conducted assuming the post- Page 21

28 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN harvest marine survival rate continues at the same percentage as the documented mean from recent years (mean = 2.66%). In a future restored condition in which the freshwater habitats provide higher survival through each life stage, the 3,500 adult coho is the recommended lowermost limit of a population goal to target for recovery. 5.2 Types and Magnitude of Restoration Needed Restoration Scenarios Analysis The Shiraz population simulation model was used to estimate the types and amount of habitat restoration needed to recover coho salmon in the Deschutes River. The Shiraz model was developed in 2008 (Anchor 2008) and updated for this analysis.. The Shiraz model was organized into seven assessment reaches for the mainstem and tributaries between Tumwater Falls (RM 2) and the upper extent of anadromous fish access (RM 41). The assessment reaches used in the model and applied in defining restoration priorities are (Figure 5, next page): Mainstem RM 2-10 Mainstem RM Mainstem RM Mainstem RM Mainstem RM Tributaries RM 2-31 Tributaries RM The Shiraz model was intentionally built and calibrated to existing data using a limited number of habitat indicators that characterize the quantity and quality of habitat supporting each life stage of coho salmon and producing predicted number of adult coho returns that track the observed numbers reported by WDFW (see Appendix A). The model was successfully calibrated to WDFW observations of the number of coho adults returning each year (see Appendix A). Since the Shiraz model was successfully calibrated to WDFW observations (Figure 6, next page), it serves as a useful tool for estimating population responses to changes in the basin, such as habitat restoration. It is important to note, that the model was intentionally designed to use a limited number of habitat indicators rather than attempting to develop a comprehensive model that incorporates the myriad of ecological variables (and interactions between variables) that affect coho survival through each life stage. As such, it needs to be acknowledged that there is substantial uncertainty when relying on the Shiraz model (or any model) to define precisely how much restoration work is needed for population recovery. Nevertheless, Shiraz is an effective tool for informing the types of restoration needed and providing a general estimate of the magnitude of restoration needed to recover the number of adult coho salmon returning to the river. Page 22

29 Number of Coho Adult Returns DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Figure 5. Shiraz Assessment Reaches 14,000 12,000 10,000 8,000 6,000 4,000 2, Adult Return Year Observed by WDFW Predicted by Model Figure 6. Comparison of Shiraz Predictions and WDFW Observations of Annual Coho Adult Returns Page 23

30 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN The Shiraz model is a population simulation analysis that allows habitat parameter inputs to be adjusted to estimate the increases in the number of adult coho returns following habitat restoration. In this way, restoration scenarios were run to assess coho population responses to different types of restoration actions in different parts of the basin. The analysis period was 2015 to For the purposes of the analysis of coho population size responses to the restoration actions, it was assumed the restoration actions were implemented in While it is not realistic to implement the restoration actions in that timeframe, it enables the analysis to be conducted with the most certainty of the population numbers at the start of the analysis period. Restoration scenarios were iteratively tested using different combinations of habitat parameter improvements. Restoration scenarios were developed using the life history approach to recovery that was described in Section 5.2 in order to identify the location and type of restoration needed to support coho in each life stage. The Shiraz outputs indicate that habitat restoration can foreseeably recover the number of coho in the strongest cohort (cohort A, i.e., returning years 2015, 2018, 2021, etc.) through restoration that targets reduction of fine sediments in the spawning areas, increases to large woody debris in rearing areas with an emphasis on tributaries and the upper mainstem, and watershed-wide reductions in the occurrence of high water temperatures and low flows. The specific habitat parameter changes are described in Table 1 and the predicted annual numbers of adult coho returns through year 2050 are presented in Figure 7 (next page). A second cohort of coho Table 1. Type and Magnitude of Habitat Restoration in Restoration Scenario A River Reach Fine Sediment (<0.85mm) Percentage LWD Percentage of Reach Meeting 25 th Percentile of LWD Counts in Reference Rivers (Fox and Bolton 2007) Habitat Parameter High Summer Temperatures Number of Days Per Year with Water Temperatures at 1000 Road Exceeding 16 o C Low Summer Flows Number of Days Per Year with Less Than 33 cfs at USGS Rainier Gage Peak Winter Flows (cfs) Mainstem RM 2-10 n/c 2% 10% n/c n/c n/c Mainstem RM n/c 0% 10% n/c n/c n/c Mainstem RM n/c 0% 10% n/c n/c n/c Mainstem RM n/c 2% 25% n/c n/c n/c Mainstem RM % 10.0% 0% 25% n/c n/c n/c Tributaries RM 2-31 n/c 1% 50% n/c n/c n/c Tributaries RM % 10.0% 60% 80% n/c n/c n/c All Reaches n/c n/c ,250 4,025 Note: n/c = no change Page 24

31 Number of Coho Adult Returns DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 2,000 1, Adult Return Year Existing Conditions Restoration Scenario A Figure 7. Predicted Coho Adult Returns in Restoration Scenario A and with the Continuation of Existing Conditions (cohort B, i.e., returning years 2016, 2019, 2022, etc.) is predicted to slowly increase in Restoration Scenario A, but the number of adults returning is fewer than 300. The third cohort (cohort C, i.e., returning years 2017, 2020, 2023, etc.) is predicted to continue through year 2050 at fewer than 30 coho adults returning in a year. Restoration of cohorts B and C appear to also require an increase in marine survival. Marine survival in this analysis includes the period from the time coho smolts migrate downstream from the smolt trap to the time they return as adults. In this way, marine survival encompasses survival through Capitol Lake, the marine phase to the ocean, and harvest upon return to coastal waters. Thus, human activities affect the marine survival rate input to the model through modification of migratory conditions in Capitol Lake and estuary, as well as through harvest upon their return. Capitol Lake was created at the mouth of the Deschutes River and severely abbreviates the estuarine transition zone for coho and other anadromous fishes. Although coho are less dependent on estuaries for rearing than other salmon, the configuration of Capitol Lake likely affects the survival of some portion of outmigrating coho through: 1) reduced fitness related to physiological stresses associated with an artificially abrupt transition to salt water, 2) predation by fish and birds throughout the lake, and 3) as described by WDFW (2008) focused predation by fish birds and mammals on juveniles and adult salmon on both sides of the physical bottleneck formed by the narrow dam opening at the mouth of the lake. The physical bottleneck and the foreseeable reduction in the fitness of outmigrating juveniles could lead to increased predation by marine mammals and other predators during the early marine life stage of coho salmon. Increased marine survival through actions such as a restored estuary at Capitol Lake, decreased early marine predation, and reduced harvest are predicted to increase coho adult return in all three cohorts. In a Restoration Scenario that assumes a 1.0% increase in marine survival in addition to the restoration actions described in Restoration Scenario A, all three cohorts are Page 25

32 Number of Coho Adult Returns DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN predicted to increase to more than 1,000 coho adults by year 2050 with the strongest cohort increasing to more than 9,000 coho adults returning (Figure 8). The approach taken to develop the restoration scenarios analyzed in Shiraz and that is recommended as a recovery strategy for the watershed is essentially a coho life history approach. The idea is to link restoration actions and locations to the life stage(s) that will benefit from them and work at a watershed-wide scale to concurrently improve the capacity and productivity of habitats for coho. The strategy is to use the habitat limiting factors information about conditions in the watershed to identify the work that is needed and to proceed during implementation with a reasonable balance among life stage benefits in order to prevent bottlenecks at any life stage. The recommended restoration strategy focuses on five main elements in the watershed: Reduce fine sediments Increase the availability of complex habitats Reduce high water temperatures Improve instream flows Improve marine survival These elements have some overlap between them, in that work to improve one specific element can be expected to provide benefits for other elements. There are variations among the elements as to the actions necessary to induce meaningful changes in the watershed that will result in the recovery of coho salmon. In the following paragraphs, each element is discussed in more detail. Reduce Fine Sediments Fine sediment in the Deschutes River and its tributaries occurs at levels that are problematic for coho salmon. While Collins (1994) and Ecology (2015) attribute a significant portion of this condition to the young geologic age of the watershed, there are additional inputs attributable to 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 2,000 1, Adult Return Year Restoration Scenario B (same as A, but includes 1.0% higher marine survival Figure 8. Predicted Coho Adult Returns in Restoration Scenario B which includes higher Marine Survival Page 26

33 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN human modifications or unknown sources (could be natural or human-induced) that need to be addressed. The fine sediment problems of the watershed are driven by excessive inputs. This effect is exacerbated by the long time it takes to flush sediments from the riverbed within the low gradient mainstem. The past loss of large wood and associated instream structure reduces the river s ability to maintain localized intermittent areas with a lower concentration of fines while the fine sediments are being flushed through the system.. The most acute need for fine sediment reduction is in the spawning grounds of the watershed. Thus, work to reduce fine sediments should focus primarily on conditions at and above the spawning areas. Given the documentation of some mainstem spawning and the expectation that additional mainstem spawning will occur as habitats are restored and coho population numbers increase, a component of the fine sediment includes sediment sources upstream of the Deschutes Falls (upper extent of anadromous zone). Increase the Availability of Complex Habitats Habitat complexity is a broad term that encompasses multiple types of habitat improvements and restoration techniques. There is a need to greatly increase the quantity and quality of pool habitats (and pool:riffle sequences), availability of instream cover, access to lower velocity offchannel habitats, sort sediments, and improve prey production. Installation of LWD can provide benefits through these multiple functions. Based on the existing lack of sufficiently large LWD in the system, improvements are needed throughout the anadromous zone of the watershed. Another aspect of increasing habitat complexity is restoration focused on reconnecting new off-channel habitats and improving conditions in existing off-channel habitats. These habitats provide lower velocity areas often with more connectivity with and shade from riparian vegetation. Related to this, it is important to keep existing LWD jams in the river (i.e., not remove them). Establishment of mature riparian vegetation to provide shade is a primary element of Ecology s draft TMDL for the watershed (Ecology 2015). Riparian vegetation contributes to habitat complexity through root structure that can provide undercut bank cover for fish and over time as a source of LWD to the river. Access to complex habitats for rearing and overwintering in tributary systems is also vital for juvenile coho. The juvenile fish need suitable passage conditions to access further in middle and lower watershed tributaries and the quality of habitat needs to be improved. These improvements can be for floodplain areas accessible during higher flows when LWD and expanded channel networks can provide low velocity habitats. Reduce High Water Temperatures For coho salmon that remain in the river for rearing through an entire summer before outmigrating the following spring, there is a substantial need to reduce the high water temperature conditions in the watershed. The high temperatures occasionally exceed lethal level, more often create thermal barriers keeping juveniles from otherwise suitable habitats, and also increase metabolic demand so more energy is put into sustaining and feeding, rather than growth. In the TMDL approach for reducing water temperatures, Ecology (2015) emphasizes Page 27

34 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN the establishment of a wide mature riparian buffer and reduced channel width to increase water depths and shading over river. An important part of establishing a mature riparian buffer is control of invasive vegetation that does not provide the functional benefits of native vegetation. Additional opportunities for reducing water temperatures are by increasing base flows which would lessen the heating effect of solar radiation and additional mature vegetation beyond the riparian zones. The Ecology (2012) analysis of the effect of increased base flows showed a relatively small incremental reduction in water temperatures. However, the analysis presented only showed one scenario with increased base flow and it was combined with multiple other parameter changes. Additional analysis with fewer variables may indicate a larger contribution resulting from increases to low flows. A key aspect of the flow contribution to water temperature is a need to keep or increase the availability of cool water sources into the river system. Where possible, efforts to have more cooler water enter the system would be beneficial and those benefits may be enhanced through appropriately sited habitat complexity projects that are located and design to increase the local benefits of a cool water source or connect cool groundwater sources with off-channel habitat. Several locations of cool water refugia (i.e., locations with cooler water temperatures than surrounding areas) were identified along the Deschutes mainstem based on thermal infrared surface water data collected for the TMDL study (Watershed Sciences 2004). In the timber lands of the upper watershed, mature vegetation conditions beyond the regulated riparian corridor would provide multiple functions, including, some contribution to the reduction of water temperatures. The additional vegetation would reduce heating as the water drains into defined tributaries with riparian buffers. Improve Instream Flows The Deschutes River endures extremes at both ends of the hydrograph as summer flows are detrimentally low and winter flows often peak too high. The summer low flows reduce habitat availability and increase water temperatures. The relationship between flows and water temperatures is widely acknowledged. Efforts to increase base flows should focus on reduction in withdrawals (through water right acquisition, prevention of unauthorized withdrawals, and voluntary conservation) and increased surface water infiltration through additional vegetation and reduced routing of water to accelerate draining (particularly in agricultural areas). Peak flows are particularly harmful because the higher they are the more scour or burial of coho salmon eggs. Studies have shown that peak flows during egg incubation to be a strong factor affecting of the number fish to survive to smolt outmigration and the higher the peak flow, the lower the smolt numbers (e.g., Seiler et al. 2004, Schueurell et al. 2006). Since spawning in the Deschutes River is largely in the upper tributaries that are surrounded by managed forested, the human influence on peak flows is less about impervious surfaces and more about the variable amount of vegetation beyond riparian buffers and the logging road network. Although the area is managed in accordance with regulations for buffer widths, additional vegetation in Page 28

35 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN the sub-basins would reduce the speed at which water is delivered to the tributaries. Clearcutting has been documented to decrease water infiltration while increasing overland flow and the volume and speed of water delivered to streams (Bull 1979 and Jones and Grant 1996, as cited in Ecology 2012). A modeling analysis by LaMarche and Lettenmaier (1998) documented a relationship between forest roads and peak flows. The modeling predicted that forest roads contributed to an approximately 5 percent increase in peak flows in mean annual and 10-year events. LaMarche and Lettenmaier (1998) also estimated a similar level of effect on peak flows if mature forests are harvested. LaMarche and Lettenmaier (1998) estimated that the combined effects of having both roads and forest harvest increased peak flows in a 10-year event by approximately 15 percent. This increase is more than the sum of the estimates for the individual variables, thus indicating a synergistic effect between logging roads and forest harvest. Peak flows at lower locations in the watershed may also contribute to sweeping juvenile fish out of overwintering habitat into less preferred areas. Restoration is needed to increase the amount of riparian vegetation along tributaries and decrease the channelization of water courses which act to accelerate water s entry to the tributaries and mainstem. Improve Marine Survival The marine survival phase for coho salmon in the Deschutes River includes two components that are directly affected by human modifications or actions. The first is the modified estuarine transition zone caused by the impoundment of Capitol Lake to replace the historic 2-mile long estuary. The second is the harvest of adult coho after their return from the Pacific Ocean. The importance of making improvements to the marine survival phase is evident from the historic trends in coho salmon returns to the river relative to marine survival. The Shiraz analysis provides additional insight on the strong influence of marine survival on the overall stability of the coho population. The Shiraz analysis showed that an ambitious watershed-wide effort to restore freshwater habitats can stabilize predicted coho returns in the strongest cohort, but only through an accompanying 1% increase in marine survival does the model predict strong signs of recovery among the two weaker cohorts. The accompanying 1% increase in post-harvest marine survival is also predicted to nearly triple the numbers of returning coho adults as the river is naturally populated (seeded) with more fish through natural spawning. The Capitol Lake impoundment creates a much more abrupt estuarine transition zone for outmigrating smolts. This abrupt transition from fresh water to salt water may reduce the fitness of the outmigrating coho and potentially affect their early marine survival. The configuration of the lake and lake outlet also foreseeably increase predation pressure on the smolts. The lake itself exposes coho smolts to freshwater predators that they otherwise would not encounter. Also, as described by WDFW (2008), the narrow dam outlet and tide gate can focus predation by fish birds and mammals on juveniles and adult salmon on both sides of the physical bottleneck formed by the narrow dam opening at the mouth of the lake. Restoring the estuary and a wider connection into Budd Inlet would be expected to improve coho smolt numbers surviving to outmigrate to the ocean. Page 29

36 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Another potential element of concern in the estuary is the presence of invasive New Zealand mud snails (Potamopyrgus antipodarum). A study has documented decreased fitness to trout consuming New Zealand mud snails when they are available as prey after infesting freshwater habitats (Vinson and Baker 2008). Upon the return of adult fish from the ocean, harvest pressure reduces the number of fish returning to the river. Data from WDFW (unpubl. data) show highly variable harvest rates of Deschutes River coho in the last 15 years ranging from 0 percent to nearly 70%. Prior to the decline in population size observed in the late 1980s, harvest rates were consistently between 65% and 75%. Based on the WDFW estimated marine survival rates pre-harvest, the numbers of returning coho adults are high enough to support an accelerated recovery of coho population numbers in the Deschutes River. Climate change was not explicitly included in the identification of a recovery strategy. However, changes associated with climate change are expected to add to the vulnerability of the Deschutes River coho population and may require additional restoration to further offset future impaired conditions related to climate change. Several of the target parameters for restoration are ones that are expected to be exacerbated by climate change, specifically low flows, peak flows, and high water temperatures Recommended Restoration Strategy The recovery strategy for coho salmon in the Deschutes River is focused on supporting their life history needs throughout the watershed. In broad terms this begins with spawning, egg incubation, and early rearing in the upper portions of the watershed and works progressively downstream to support later stages of the freshwater life history of the juvenile coho. The upper tributaries between RM 31 and RM 41 (e.g., Thurston, Johnson, Huckleberry, Mitchell, Fall, and Pipeline Creeks) provide the principal spawning habitat for coho salmon. While these tributaries have been affected by past events, the lowermost portions currently appear to have largely recovered from these historic impacts. The mainstem Deschutes in the vicinity of these upper tributaries (RM 31-41) has limited suitable rearing habitat for juvenile coho and experiences thermal conditions that are sub-optimal during the summer months likely caused by a lack of riparian shade and low flows. The middle and lower portions of the mainstem (i.e., RM 2-31) also offer limited juvenile coho rearing habitat because it is an extended area providing only a simplified channel profile, primarily caused by a lack of LWD, particularly key size pieces, and limited off-channel rearing habitat for juvenile coho. There are relatively few substantial tributaries in the middle and lower Deschutes and habitat conditions in the tributaries are impacted by reduced habitat complexity from LWD, cleared riparian areas, impaired water quality, and restricted access to potential rearing habitat. Finally, once the coho smolts outmigrate from the river, they encounter a severely abbreviated estuarine transition zone into salt water due to the conversion of the river estuary into an impounded lake. The work to restore habitats in the Deschutes River watershed and recover coho salmon will require many different types of action. Several types of restoration actions are identified for Page 30

37 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN each analysis reach. Protection is also a key aspect of this recovery work. It is imperative to protect the areas that are functioning well. Protection through acquisition can also provide substantial opportunities to do meaningful restoration without the constraints that restoration on others land sometimes presents. The recovery work identified in this Plan is well aligned with other efforts, notably Ecology s TMDL. The work will entail large-scale efforts with additional progress made through generally smaller efforts that include grass roots initiatives and community outreach and education. Upper Tributaries RM Priority: Highest Life Stages: Spawning, egg incubation, rearing, and overwintering The upper tributaries support most of the coho spawning in the watershed. Based on WDFW spawning data from 1980 through 2014, the most utilized creeks for spawning, in order, are Huckleberry Creek, Johnson Creek, Thurston Creek, and Mitchell Creek. Although since 1990, more coho adults have been observed in Thurston Creek than Johnson Creek. These tributaries are largely in managed forest areas and have been vulnerable to damaging landslides and debris flows. Given the limited spatial distribution of spawning in the watershed and the critically low adult returns for two of the cohorts, restoration work in the upper tributaries is the highest priority in the basin. In addition to the spawning, the tributaries provide key habitat for juvenile rearing and Sullivan et al. (1987) indicates that a portion of the fish overwinter in the upper tributaries. The coho rearing study conducted by the Squaxin Island Tribe in 2012 to 2014 found that hatchery coho juveniles released high in the basin relocated in the watershed and were found most consistently in the tributaries and mainstem habitats between RM (Steltzner pers. comm.). The study also observed that coho juveniles were only present if LWD was available at the site for cover. The study focused on mainstem locations identified as providing cooler water from springs, but did not locate any coho in those areas unless LWD was also available. The restoration work in the upper tributaries includes instream actions as well as broader subbasin scale needs. The broader sub-basin scale needs include reducing fine sediment inputs from steep areas vulnerable to landslides and the logging road network; expanding the extent of the area removed from timber harvest either through purchasing wider buffer areas or entire tributary basins. Based on aerial imagery, the upper tributaries have been extensively logged since 1990 with much of the logging occurring since As the forest regrows in the upper tributaries, there may be opportunities for adjusting forest management or land acquisition in these sensitive tributaries. These broader actions would improve conditions for fine sediments, water temperatures, and instream flows. As described above in Section 4.1.5, fine sediment reductions can be achieved more rapidly in tributaries than mainstem areas. Efforts in and along the tributaries should focus on increasing the availability of LWD in the spawning and rearing portions of the creek. The added LWD should include key pieces that are of sufficient size to scour pools and be stable over a long period (generally inch diameter Page 31

38 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN will be suitable for the range of channel sizes in headwater tributaries). The additional LWD will add habitat complexity by providing additional pool:riffle sequences which are utilized for rearing and spawning. The movement of water past LWD structures will also cause localized scour which will move fine grained materials downstream and act to sort larger substrate sizes and provide favorable spawning substrates in pool tailouts. Upper Mainstem RM Priority: High Life Stages: Rearing, spawning, and egg incubation Other than the upper tributaries, most of the remainder of the documented coho spawning has in the upper mainstem between RM 31 and RM41. As such, these habitats are encountered by juvenile coho dispersing from natal areas at relatively small sizes. As described above, the coho rearing study conducted by the Squaxin Island Tribe in 2012 to 2014 found that hatchery coho juveniles released for the study were observed most consistently in the tributaries and mainstem habitats between RM (Steltzner pers. comm.). The availability of cooler water associated with a spring did not result in observations of coho in those areas unless LWD was available for cover. This mainstem reach is a high priority for restoration and protection because of its high utilization potential by coho and the adjacent land uses which may provide opportunities to aggressively improve habitat conditions. Although the study area ended at the upper extent of the anadromous zone, the uppermost portions of the watershed (i.e., upstream of RM 41) affect these downstream areas. Therefore, opportunities to restore conditions above the anadromous zone will also improve habitat conditions for coho, particularly through reducing fine sediments, shade water, and provide long-term wood recruitment to the river. This reach currently lacks sufficient quantities of LWD and therefore is not afforded the benefits that extensive wood can provide in terms of habitat complexity (e.g., pool:riffle sequences, offchannel habitats, potential thermal stratification in scour holes), habitat stability, and cover for coho. The installation of LWD structures can also narrow wetted widths through scour that creates more channel depth and a more pronounced thalweg. This is a priority type of action identified by Ecology in the draft TMDL implementation plan for the watershed (Ecology 2015). The upper mainstem is identified by Ecology as needing the largest reductions in wetted widths and coincides with the reach identified as having the highest surface water temperatures in the basin during an August 2003 thermal infrared remote sensing survey of surface temperatures (Watershed Sciences 2004). This reach and the next reach downstream are the two mainstem reaches recommended from the Shiraz analysis for the highest amounts of LWD to be installed due to the proximity to the spawning areas. Restoration and protection in the reach should focus on providing habitat complexity and stability at locations most likely utilized by coho salmon, such as at the mouth of spawning tributaries, cool water sources, and off-channel habitat areas. Bars and side channels have formed near the mouths of several tributaries with notable spawning habitat. These are highly beneficial areas to work to establish or stabilize side channel networks. The river habitat would Page 32

39 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN be improved by stability provided by the addition of LWD structures at key locations. Increased stability will maintain existing off channel habitats and will provide the opportunity for native woody vegetation to get established. This riparian vegetation will provide shade to the main channel and off-channels and over time add to site stability and LWD recruitment. Ecology (2012) identified a series of springs in this reach that provide cooler temperatures and therefore more favorable habitat for juvenile coho. The springs were located at RM 38.5, 38.4, 37.3, 36.5, and The placement of LWD included in the restoration described above and other actions should be taken to reduce fine sediment inputs in this reach. Based on the Ecology s (2012) TMDL analysis, the area between RM 31.4 and 35.4, from Fall Creek downstream towards Pipeline Creek has a substantial need for fine sediment input reduction (32% reduction needed to achieve target) in the watershed. Raines (2007) reports most fine sediment in the reach between occurring in order from highest in RM 34, 35, 38, and 39. Although full restoration of fine sediment levels in mainstem areas is a massive, long-term effort (see Section 4.1.5), reductions should be pursued through efforts to reduce sources to the upper mainstem (including watershed areas upstream of Deschutes Falls) as well as improve fine sediment mobilization and sorting to provide pockets of good egg incubation conditions in the upper mainstem. Protection of intact habitats with well-vegetated riparian vegetation is an important tool to prevent any increased fine sediment inputs. Opportunities to reduce water withdrawals should be investigated to improve base flow conditions and contribute to reduced water temperatures. Since this is the highest mainstem reach, actions in this reach will have the most far-reaching benefits downstream through the river. Tributaries RM 2-31 Priority: High Life Stages: Rearing, overwintering, limited spawning, and egg incubation Tributary habitat is particularly important for coho salmon rearing and overwintering in the Deschutes River. While many coho juveniles remain in their natal tributaries in the upper watershed, particularly early in their rearing stage, a portion of the population disperses into the mainstem and moves downstream to other rearing habitats. Given the high temperatures in the mainstem during summer months and the limited quantities of LWD present to provide cover, the tributaries in the middle and lower portions of the river (RM 2-31) can provide more hospitable conditions for coho. In addition, the tributaries provide access to wetlands, beaver ponds, and other low velocity habitats that coho use for overwintering. The Squaxin Island Tribe s coho rearing study documented some coho juvenile use of tributary habitats between RM 2-31, while no coho were observed in mainstem habitats between RM 2-31 (Steltzner pers. comm.). Sullivan et al. (1987) documented overwintering coho in several tributaries in this part of the river. Page 33

40 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Restoration and protection of tributaries between RM 2-31 is a high priority in the watershed. It is recommended that restoration and protection efforts focus first on creeks documented by Sullivan et al. (1987) as being used in high numbers (>100 coho) during winter surveys. This includes the following tributaries Silver Springs ( ), Spurgeon Creek ( ), Turner Spring ( ), and Ayer/Elwanger ( ). However, even though the Sullivan et al. (1987) report provides the best information available on coho overwintering, the data are limited and things may have changed over the last 30 years old such that there is good justification to adjust the list of target tributaries to work on. Given the increasing agricultural and development pressure as one moves lower in the watershed, protection of tributary habitats is an important need. This is particularly true for cool water sources, tributary mouths, and overwintering habitats. It is recommended to take a balanced approach depending on the opportunities of the tributary subwatershed such that efforts are undertaken to restore the lower creek sections and higher areas within tributaries that can provide overwintering habitat. To improve overwinter rearing conditions, focus on Sullivan streams and other areas with wetland areas and beaver ponds that could be improved (access, structure, shading, invasive veg removal) to provide additional overwintering habitat. Efforts should be taken to reduce water withdrawals, particularly from cool water sources, in the tributaries. Efforts to increase base flows should focus on reduction in withdrawals (through water right acquisition, prevention of unauthorized withdrawals, and voluntary conservation) and increased surface water infiltration through additional vegetation and reduced routing of water to accelerate draining (particularly in agricultural areas). Spurgeon Creek is the longest and largest tributary in this portion of the Deschutes. The creek flows into the mainstem at RM 10. Coho salmon spawning has been historically documented in Spurgeon Creek, although there has been no survey effort since coho numbers declined in the late 1980 s (WDFW 2015). Spurgeon Creek habitat for rearing would be improved by removing barriers for juvenile coho to access wetlands, adding instream structure to provide cover and habitat complexity at higher and lower flows, and increasing the extent of mature riparian vegetation. Silver Spring and Turner Spring both provide cool water refuge habitat for juvenile coho salmon. These water sources should be protected and restoration added to improve habitat conditions in those areas. Restoration including LWD and improved riparian conditions would be most beneficial. The tributary connecting Lake Lawrence to the mainstem at RM 28.7 has been substantially altered by ranching activities which have led to the removal of riparian vegetation and the ditching of the outlet channel. Habitat restoration planning is underway for the upper portion of the tributary, including restoring habitat watered by a cool spring. Additional restoration is needed in the lowermost reaches of the tributary, including its outlet to the mainstem. The water from Lake Lawrence is particularly warm in the summer. The outlet of the lake could potentially be modified to have the lake drain deeper, cooler water rather than the surface Page 34

41 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN water. However, more information is needed on temperature stratification in the lake and the possible engineering requirements necessary to draw any cooler water that may be available. Reichel Creek appears to be a highly modified system that flows into the mainstem at RM The Reichel Creek system includes large areas of wetland habitat that could potentially be improved for coho rearing and overwintering. Restoration of any fish passage blockages on the lower creek would increase coho access the creek and wetland habitats. Such fish passage efforts should be coordinated with efforts to remeander the creek, add LWD for instream structure, and add riparian vegetation. Chambers Creek located at RM 4.7 is a fairly long tributary in the lower river. It is a highly modified system in its middle and upper reaches, as the creek system includes shallow lakes, agricultural and residential land uses that restrict the creek s alignment and a lack of riparian vegetation. Some enhancement through riparian vegetation restoration would be beneficial. The lower parts of the system provide more opportunities in low gradient wetland areas that could be improved to provide better habitat. Fish access through culverts may also need to be improved. Additional information on flow and water quality conditions in the creek system would be needed to inform potential value of habitat for juvenile coho rearing and overwintering. Mainstem RM Priority: Moderate Life Stages: Rearing Conditions in the mainstem between RM are similar to those in RM although the land use transitions to more agriculture and residential. This reach is more separated from the spawning grounds and encountered slightly later during juvenile coho s dispersal into downstream habitats of rearing and overwintering; therefore, it is considered of lesser priority. This reach is identified as a moderate priority for restoration and protection. Similar to all other mainstem reaches, the Mainstem RM reach currently lacks sufficient quantities of LWD and therefore is not afforded the benefits that extensive wood can provide in terms of habitat complexity (e.g., pool:riffle sequences, off-channel habitats, potential thermal stratification in scour holes), habitat stability, and cover for coho. The installation of LWD structures can also narrow wetted widths through scour that creates more channel depth and a more pronounced thalweg. This is a priority type of action identified by Ecology in the draft TMDL implementation plan for the watershed in order to reduce water temperatures (Ecology 2015). The thermal infrared temperature survey in August 2004 indicated that surface water temperatures in this reach are among the highest in the watershed (Watershed Sciences 2004). Ecology (2012) identified only a couple cool water sources in the reach: a side channel at RM 30.1 and the Lake Lawrence tributary at RM This reach and the next reach upstream are the two mainstem reaches recommended for the highest amounts of LWD to be installed due to the proximity to the spawning areas. There is a particular need for restoration to reduce water temperatures in the reach between the top of the reach and Lake Lawrence. In addition to the Page 35

42 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN installation of LWD to reduce channel widths, there is a significant need to add riparian vegetation to increase streambank stability and provide shade. Restoration and protection in the reach should focus on providing habitat complexity and stability at locations most likely utilized by coho salmon, such as at the mouth of the limited number of tributaries in the reach, cool water sources, and off-channel habitat areas. The river habitat would be improved by stability provided by the addition of LWD structures at key locations. The stability will maintain existing off channel habitats and will provide the opportunity for native woody vegetation to get established. This riparian vegetation with provide shade to the main channel and off-channels and over time add to site stability and LWD recruitment. The placement of LWD included in the restoration described above and other actions should be taken to reduce fine sediment inputs in this reach. Based on the Ecology s (2012) TMDL analysis, the mainstem area just upstream of the Lake Lawrence tributary (between RM 28.8 and 30.4) has a substantial need for fine sediment input reduction (30% reduction needed to achieve target) in the watershed. Raines (2007) reports most fine sediment in the reach between occurring in order from highest along RM 27 and RM 25. Opportunities to reduce water withdrawals should be investigated to improve base flow conditions and contribute to reduced water temperatures. Since this is the highest mainstem reach, actions in this reach will have the most far-reaching benefits downstream through the river. Mainstem RM Priority: Low Life Stages: Rearing Conditions in the mainstem between RM are similar to those in RM 31-41, although the land use transitions to more agriculture and residential in the lowest portion of the reach. Moving downstream through the mainstem reaches, the distance between the habitats and the spawning grounds gets greater and greater. The Squaxin Island Tribe s coho rearing study did not find any juvenile coho salmon at the mainstem stations surveyed in this reach (Steltzner pers. comm.). This reach is identified as a low priority for restoration and protection relative to other reaches in the watershed. The upper three miles of this reach were identified by Ecology as needing among the largest reductions in wetted widths in order to improve water temperatures (Ecology 2015). Ecology (2012) identified only a couple cool water sources in the reach: spring at RM 24.4 and a spring at RM This reach and all downstream mainstem reaches are recommended for a lesser amount of LWD placement than upstream reaches, but substantial restoration efforts are needed to achieve the lesser targets identified in Restoration Scenario A. Page 36

43 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Based on the Ecology s (2012) TMDL analysis, the mainstem area between RM 20.8 and RM 24.4 has the second highest percent reduction (41 percent) needed to achieve fine sediment input targets in the watershed. Raines (2007) reports most fine sediment in the reach between occurring in order from highest along RM 17, 18, and 24. Mainstem RM Priority: Low Life Stages: Rearing Conditions in the mainstem between RM are similar to those in RM 17-25, although the alterations of the reach are more related to agriculture. Moving downstream through the mainstem reaches, the distance between the habitats and the spawning grounds gets greater and greater. The Squaxin Island Tribe s coho rearing study did not find any juvenile coho salmon at the mainstem stations surveyed in this reach (Steltzner pers. comm.). This reach is identified as a low priority for restoration and protection relative to other reaches in the watershed. This reach was identified by Ecology as needing among the largest reductions in wetted widths in order to improve water temperatures (Ecology 2015). Ecology (2012) identified only a couple cool water sources in the reach: tributary at RM 16.4 and a spring at RM This reach and adjacent mainstem reaches are recommended for a lesser amount of LWD placement than upstream reaches, but substantial restoration efforts are needed to achieve the lesser targets identified in Restoration Scenario A. Based on the Ecology s (2012) TMDL analysis, the mainstem area between RM 20.8 and RM 24.4 has the third highest (out of five) percent reduction (40 percent) needed to achieve fine sediment input targets in the watershed. Raines (2007) found this reach to be delivering the lowest amount of fine sediment reach from Mainstem RM 2-10 Priority: Low Life Stages: Rearing Conditions in the mainstem between RM 2-10 are similar to those in RM 10-17, although the land use transitions to more urban and residential areas. Moving downstream through the mainstem reaches, the distance between the habitats and the spawning grounds gets greater and greater. The Squaxin Island Tribe s coho rearing study did not find any juvenile coho salmon at the mainstem stations surveyed in this reach (Steltzner pers. comm.). This reach is identified as a low priority for restoration and protection relative to other reaches in the watershed. This reach was identified by Ecology as needing among the largest reductions in wetted widths in order to improve water temperatures (Ecology 2015). Ecology (2012) identified only one cool water source in the reach: spring at RM 3.1. This reach and the next two upstream mainstem Page 37

44 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN reaches are recommended for a lesser amount of LWD placement than upstream reaches, but substantial restoration efforts are needed to achieve the lesser targets identified in Restoration Scenario A. Based on the Ecology s (2012) TMDL analysis, the mainstem area between RM 20.8 and RM 24.4 has the highest percent reduction (46 percent) needed to achieve fine sediment input targets in the watershed. Raines (2007) reports most fine sediment in the reach between occurring in order from highest along RM 3, 2, 4, 6, 7, and 5. Marine Survival Priority: High Life Stages: Outmigrating smolts and returning adults As shown in the Shiraz analysis, marine survival rates are a major factor affecting coho population abundance in the Deschutes River. The marine survival phase for coho salmon in the Deschutes River includes two components that are directly affected by human modifications or actions. The first is the modified estuarine transition zone caused by the impoundment of Capitol Lake to replace the historic 2-mile long estuary. The second is the harvest of adult coho after their return from the Pacific Ocean. Both of these actions are recommended as high priorities for restoring the coho salmon population in the Deschutes River. 5.3 Map and Database of Restoration Opportunities A GIS database was prepared to compile the existing information on the 343 reaches surveyed by Cramer (1997). Additional information was appended to identify tributary mouths, coho rearing study data, and habitat restoration opportunities. Examples of habitat restoration opportunities described above are presented in Figures 9 through 17. These maps are intended to help show the types and locations of priority restoration opportunities in the watershed. These are not intended to be an exhaustive presentation of priorities, rather a visual depiction of representative projects that could contribute meaningfully to coho salmon recovery. Protection opportunities need to be identified and pursued as well. The restoration opportunities described can also be thought of as describing the types of conditions that should be priorities for protection in those areas where those conditions are currently provided. Page 38

45 Restore mainstem habitats at or near the mouth of spawning tributaries to provide complex habitat with instream wood for cover and pool habitat, riparian vegetation for shading, and side channels. At the mouth of Thurston Creek (shown) there is pool and side channel habitat that would be improved by placement of ELJs with key sized logs to stabilize the habitats and provide stable areas for woody riparian vegetation to grow and shade the river. Add instream structure through large wood placement, including key pieces, to slow inputs of fine sediments from eroding banks, especially above spawning areas. Plant wider riparian buffers to provide shade, slow surface runoff, reduce fine sediment inputs, stabilize banks, and provide long term wood recruitment to tributary and mainstem habitats. Huckleberry Creek and other spawning tributaries would be improved by more instream wood for cover, habitat complexity, and gravel sorting Figure 9. Examples of priority restoration actions in the Deschutes River watershed between river mile 38 41

46 Install ELJs with key pieces to add stability to side channel habitats and limit channel migration. This will ensure the availability of side channel habitats and provide the opportunity for woody riparian vegetation to grow to provide shade to the aquatic habitats. Restore mainstem habitats through ELJ placement including key LWD pieces to provide more complex habitat (pool:riffle sequences), scour a distinct thalweg, and reduce channel width. This type of restoration is needed at reach scales to improve what is currently extended areas with simple channel planform geometry. The large wood will also provide important instream cover for coho. Restore mainstem habitats at or near the mouth of spawning tributaries to provide complex habitat with instream wood for cover and pool habitat, riparian vegetation for shading, and side channels. Downstream of the mouth of Fall Creek (shown) there are braided channels that would be improved by placement of ELJs with key sized logs to stabilize the habitats, limit channel migration, and provide stable areas for woody riparian vegetation to grow and shade the river. Similar opportunities are possible at the mouth of Mitchell Creek. Figure 10. Examples of priority restoration actions in the Deschutes River watershed between river mile 34 38

47 Install ELJs with key pieces to add stability to side channel habitats and limit channel migration. This will ensure the availability of side channel habitats and provide the opportunity for woody riparian vegetation to grow to provide shade to the aquatic habitats. Prioritize this work initially in areas identified as providing cool water refuge. Plant wider riparian buffers for shade, bank stabilization, and other beneficial functions. Ensure/restore fish access to wetlands and restore wetland habitats to provide cool, clean water and good rearing and overwintering habitat for coho. Ponded areas created by beaver dams tend to be highly utilized by salmon and beavers can contribute significantly to restoration efforts in tributaries and side channels. Figure 11. Examples of priority restoration actions in the Deschutes River watershed between river mile 29 34

48 Assess potential for wetland access or improvement of access for coho. There is also a potential opportunity to improve wetland habitat quality. The Reichel Creek system has the potential to be substantially improved for coho. Fish passage at multiple water crossings should be provided. Placement of large wood would provide habitat complexity, sort gravels, and provide cover for coho. Remeander the tributary to provide additional aquatic habitat and restore wider riparian buffers for shade and other functions. The system includes extensive wetlands that could be restored to provide improved habitat for coho. Add instream wood to tributary habitats and remeander straightened channel alignments to provide more rearing habitat of higher quality for juveniles. The instream wood will provide cover. Plant wide riparian buffers including along bank edges to provide shade, stabilize banks, and reduce sediment inputs. The Lake Lawrence outlet channel (shown) can be restored to improve fish habitat through these techniques and facilitate fish passage to habitats being restored higher in the tributary. Figure 12. Examples of priority restoration actions in the Deschutes River watershed between river mile 25 29

49 Install ELJs with key pieces to encourage off channel flow and add key sized wood within old meander scars. Figure 13. Examples of priority restoration actions in the Deschutes River watershed between river mile 21 25

50 Protect and restore tributary habitats and water quality, particularly cool water sources such as Silver Spring (shown). Add instream wood at lower locations to provide cover for coho. Plant wide riparian buffers including along bank edges to provide shade, stabilize banks, and reduce sediment inputs. Where possible, allow beavers to build dams and pond water that can provide good rearing and overwintering habitat for coho. Restore mainstem habitats through ELJ placement including key LWD pieces to provide more complex habitat (pool:riffle sequences) and instream cover for coho. Restore habitats at or near the tributary mouth. Install ELJs with key sized logs to create a scour pool and provide complex habitat with instream wood cover. Restore mainstem habitats through ELJ placement including key LWD pieces to provide more complex habitat (pool:riffle sequences), scour a distinct thalweg, and reduce channel width. This type of restoration is needed at reach scales to improve what is currently extended areas with simple channel planform geometry. The large wood will also provide important instream cover for coho. Plant wider riparian buffers, including conifers, to provide shade, terrestrial prey inputs, and other functions. Figure 14. Examples of priority restoration actions in the Deschutes River watershed between river mile

51 Install ELJs including key sized logs to provide scour pool at mouth of cool water tributary and other cool water areas. The instream wood will provide cover for coho. Install ELJs including key sized logs to promote establish of side channel through meander cutoff channel and provide stable habitat for woody riparian vegetation to grow and shade the river. Plant riparian vegetation to promote bank stabilization, provide shade to river, and provide other functions. Figure 15. Examples of priority restoration actions in the Deschutes River watershed between river mile

52 Add wood and restore woody vegetation to riparian corridor and wetland. Spurgeon Creek is an important rearing and overwintering tributary for juvenile coho and coho spawning has been documented. Where possible, allow beavers to build dams and pond water that can provide good rearing and overwintering habitat for coho. Install ELJs including key sized logs to promote establish of side channel through meander cutoff channel and provide stable habitat for woody riparian vegetation to grow and shade the river. Plant riparian vegetation to promote bank stabilization, provide shade to river, and provide other functions. Figure 16. Examples of priority restoration actions in the Deschutes River watershed between river mile 7 12

53 Restore mainstem habitats through ELJ placement including key LWD pieces to provide more complex habitat (pool:riffle sequences) and instream cover. Plant wider riparian buffers to provide shade to river. Capitol Lake is just downstream and restoring the estuary is part of the High Priority assigned to Marine Survival Install ELJs including key sized logs to provide scour pool at mouth of cool water tributary and other cool water areas. The instream wood will provide cover for coho. Assess and improve, if necessary, fish access into wetland habitat. Figure 17. Examples of priority restoration actions in the Deschutes River watershed between river mile 2 7

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55 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN 5.4 Estimated Quantity of Restoration Needed Preliminary planning level estimates were prepared for the amount of restoration work called for in this analysis. The estimate is based on three primary components of the recovery plan: Placement of large wood to form instream habitat Riparian planting Bank Stabilization to reduce fine sediment inputs Each of these plan components is discussed below including the rationale for including the actions in the plan Placement of Large Wood to Form Instream Habitat Placement of large wood to form instream habitat provides multiple benefits for biological recovery. Large wood in channels forms structure that creates hydraulic diversity, forms pools, and promotes sediment storage. Increased channel complexity makes a channel more resilient in response to sediment inputs. Hydraulic diversity promotes sediment sorting and creates pockets with suitable substrate characteristics even when there is an abundance of sediment in transport. Large wood provides instream cover for fish and refugia during periods of high flow. Increased channel roughness helps reduce temperatures by increase flow depth. The Shiraz habitat model was used to determine the locations and amount of wood loading to achieve high quality habitat conditions in line with wood loading rates published by Fox and Bolton (2007) for selected reaches of the river and tributaries. Target wood loading rates by river reach including tributaries are shown in Table 2. Table 2. Target Large Wood Loading Quantities by River Reach Percent Reach Length (ft) of Stream- Length Meeting Target Length (ft) Currently Meeting Target Target Percent of Length Meeting LWD Target Target Length Length Requiring Restoration Target LWD Pieces per 328 ft Number of 328 ft Long Stream Segments Requiring Restoration Total Number of LWD Pieces to Add to Reach Mainstem RM ,240 2% % 4,224 3, Mainstem RM ,960 0% 0 10% 3,696 3, Mainstem RM ,240 0% 0 10% 4,224 4, Mainstem RM ,680 2% % 7,920 7, Mainstem RM ,800 0% 0 25% 13,200 13, ,189 Tribs RM ,664 1% % 32,432 31, ,522 Tribs RM ,683 60% 39,410 80% 52,547 13, ,066 Page 48

56 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Riparian Planting The draft TMDL report (Ecology 2015) identifies the preservation of existing forested streamside vegetation corridors and establishment of fully mature forested corridors along the Deschutes River and its tributaries as the most critical implementation actions for addressing water temperature. Riparian corridors along tributaries on managed forest lands are subject to the Washington Forests and Fish regulations. Aerial photograph review shows forested buffers exist along tributaries in the upper watershed with some gaps. The TMDL Technical Report (Ecology 2012) presents results of a shade modeling effort comparing existing conditions shade of the mainstem Deschutes River to shade conditions that would result from fully mature riparian vegetation along approximately 40 miles of the river. Figure 60 (page 136) in the TMDL Technical Report (Ecology 2012) displays effective shade targets for the Deschutes River compared to current conditions for the 70 km reach extending downstream from Deschutes Falls. Confluence used this table to estimate an approximate total shade deficiency of 28.3 percent. This percentage reflects effective shade. The riparian corridor along the Deschutes River includes variable forested conditions ranging from zero to fully mature. For the purpose of this cost estimate the effective shade deficiency is used to develop an area estimate for riparian planting. The actual area may be more than this estimate, but per acre costs would be less for a partially forested corridor. This approach provides a rational rough estimate for the amount of planting required to achieve a fully mature riparian corridor along the mainstem. The TMDL Technical Report (Ecology 2012) defines a fully mature riparian corridor as a zone 100 meters (328 ft) wide on each bank of the mainstem to provide shade, maintain a microclimate, and provide a suite of other habitat and water quality functions. Between RM 2 and RM 41, the total area of such a corridor would be approximately 3,100 acres. Using the shade deficiency as an approximation, riparian planting would be needed to reforest approximately 877 acres distributed along the mainstem river corridor. The TMDL technical report (Ecology 2012) states that full mature riparian shade is needed on 14 of the tributaries (listed in Table 26, page 138). Private timberland managers are required to comply with the Washington Forests and Fish rules, which are presumed to comply with water quality standards subject to monitoring. This estimate does not include any costs associated with expanding existing riparian corridors along the tributaries on managed private timber lands Bank Stabilization to Reduce Fine Sediment Inputs Bank stabilization along the Deschutes River mainstem would reduce some of the net contribution of fine sediment to the system as well as reduce the amount of fine sediment in transport. These reductions would result in a lower concentration of fine sediment in the riverbed on both short-term and long-term time scales. Raines (2008) reported that measurable bank erosion from 1991 to 2003 involved 192 sites and 70 acres. This number of sites may be used to estimate the approximate cost of system wide bank stabilization. Page 49

57 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Long-term bank stability and resistance to erosion improves with the establishment of fully mature riparian forests. For the near term, channel migration and bank erosion may be curbed by bank stabilization measures. For the purpose of this estimate, it is assumed that placement of large wood either as log jams or other structures may be used to enhance bank stability. This approach has the added benefit of increasing channel complexity and enhancing instream habitat. 6 SUMMARY AND RECOMMENDATIONS Coho salmon numbers in the Deschutes River have declined precipitously since the 1980 s such that two of the three brood lines are considered virtually extinct by WDFW. This analysis applied available information on habitat conditions in the watershed and knowledge of coho life cycle, habitat utilization, and habitat requirements to identify a restoration plan to recover the coho population in the watershed. Population simulation was conducted using the Shiraz model and provided an analytical tool to estimate the coho population size over time if certain levels of restoration were conducted to improve the habitat condition indicators. By iteratively adjusting the amount of restoration conducted, a restoration scenario was identified to provide a general estimate of the magnitude of restoration needed. This analysis indicated that a stable self-sustained population of coho salmon is not possible until substantial restoration is in place, but this would only stabilize the strongest cohort of coho. Recovery of the two weaker brood lines can be expected to require more than just freshwater restoration. Based on the Shiraz modeling, restoration of all three brood lines will also require improved marine survival through actions such as the restoration of the Deschutes estuary, reduction of marine mammal predation during the early marine migration of outmigrating coho, and reduced harvest pressure. The restoration components of this plan provide incremental benefits such that each action contributes to the ultimate recovery. The recommended recovery strategy focuses on five main elements in the watershed: Reduce fine sediments Increase the availability of complex habitats (increased LWD, pool:riffle sequences, offchannel habitat, riparian vegetation) Reduce high water temperatures Improve instream flows (both low flows and peak flows) Improve marine survival (both estuarine transition zone and harvest effects) This information on the types of restoration needed and the Shiraz analysis information on the scale and locations of restoration needs were applied to a coho life history approach to assign a range of priorities to different reaches of the mainstem and tributaries. Achieving these restoration targets will require both restoration and protection. In addition to large-scale projects, smaller efforts and community outreach and awareness are important for making progress throughout the watershed and by different contributing partners. In practice, habitat restoration and protection includes a large degree of opportunism when sites and funds become Page 50

58 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN available. This plan may be used to inform decisions by referring to relative priority when there are multiple opportunities and limited funds. In other situations when restoration opportunities and funding become available, the priorities assigned in this plan are not intended to discourage moving forward with an action that is aligned with any of the recommendations in this plan regardless of priority. The following reach priorities were identified: Upper Tributaries RM highest priority Upper Mainstem RM high priority Tributaries RM 2-31 high priority Mainstem RM moderate priority Mainstem RM low priority Mainstem RM low priority Mainstem RM 2-10 low priority This analysis has identified that a substantial amount of freshwater restoration and protection is necessary to recover coho salmon and that freshwater restoration alone is unlikely to result in strong increases in two of the three cohorts. Funding the amount of work needed will be challenging, particularly because the coho population is comprised of naturally spawning fish originating from a hatchery stock. It is important to take steps towards restoration of the watershed to support coho salmon. The restoration and protection work called for is well aligned with ongoing efforts in the watershed (e.g., Ecology s TMDL Implementation Plan). Given the vulnerable status of the coho population in the Deschutes River, significant action should be pursued. The most significant restoration need is to improve habitat conditions in the upper tributaries and reduce the potential for episodic degradation such as occurred in Huckleberry Creek and others in A large scale action that would be a meaningful step in coho recovery would be the acquisition of land or timber harvest rights in portions of the upper watershed along strategic spawning tributaries in order to expand riparian buffers, revegetate more of the sub-basin, and remove roads and water crossings. The priorities would be Huckleberry, Thurston, Johnson, and Mitchell Creeks. These tributaries are in managed forests. While these forests appear compliant with applicable forest management regulations, additional riparian buffer widths and vegetation throughout the sub-basins would be beneficial. A substantial portion of these watersheds appears to have been harvested within the last 15 years, so there is some time before the next harvest cycle to implement protections. This is not a recommendation to request that the landowner voluntarily adjusts harvest practices. Instead, the recommendation is to pursue the purchase of land or strategic timber harvest rights in these areas. The freshwater recovery work described in this plan needs to be coupled with actions to improve marine survival. It is necessary to look beyond the freshwater actions only because as shown by the Shiraz analysis, marine survival has a significant effect on the spawning numbers in the river. Marine survival includes all parts of the life cycle from the time the smolts outmigrate past Tumwater Falls until they return to the river as adults. Actions to provide a restored estuarine transition are highly recommended due to anticipated benefits related to a Page 51

59 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN more gradual transition from fresh water to salt water, expanded estuarine foraging opportunities, and reduced predation pressure through Capitol Lake and the tide gate at the 5 th Avenue dam. There are potentially opportunities to reduce predation by marine mammals, piscivorous fish, and birds during the early marine life stage as the outmigrating coho enter Budd Inlet and south Puget Sound. Harvest rates are another contributing factor affecting the number of coho adults returning to the river. Reduced harvest rates would increase fish returns. 7 REFERENCES Agua Tierra Environmental Consulting (ATEC) Deschutes River Reach Scale Analysis and Habitat Survey Final Data Report. Prepared for Thurston County Water and Waste Management. Anchor (Anchor Environmental, LLC) Final Deschutes River Watershed Recovery Plan: Effects of Watershed Habitat Conditions on Coho Salmon Production. Prepared for Squaxin Island Tribe Natural Resources Department, Shelton, WA. Bash, J., C. Berman, and S. Bolton Effects of Turbidity and Suspended Solids on Salmonids Final Research Report. Prepared by University of Washington, Washington State Transportation Center, and Washington State Department of Transportation. Prepared for Washington State Transportation Commission and U.S. Department of Transportation. Research Project T1803, Task 42. Bilby, R.E Contributions of road surface sediment to a western Washington stream. Forest Science 31(4): As cited in Sullivan et al (once this says as cited in but another time it doesn t) Bilby, R.E. and J.W. Ward Changes in characteristics and function of woody debris with increasing size of streams in Western Washington. Transactions of the American Fisheries Society 118: Bisson, P. A., R. E. Bilby, M. D. Bryant, C. A. Dolloff, G. B. Grette, R. A. House, M. L. Murphy, K. V. Koski, and J. R. Sedell Large woody debris in forested streams in the Pacific Northwest: past, present and future. Pages in E.O. Salo and T.W. Cundy, editors. Streamside Management Forestry and Fishery Interactions. Univ. of Wash., Institute for Forest Resources, Contribution 57, Seattle, WA. Bjornn, J. R., and D. W. Reiser Habitat requirements of salmonids in streams. In W. R. Meehan (ed.), Influence of forest and rangeland management on salmonid fishes and habitats, p Special Publ. 19. American Fisheries Society, Bethesda, MD. Carter, K The Effects of Temperature on Steelhead Trout, Coho Salmon, and Chinook Salmon Biology and Function by Life Stage. Page 52

60 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Chapman, D.W Critical Review of Variables Used to Define Effects of Fines in Redds of Large Salmonids. Transactions of the American Fisheries Society 117: Collins, Brian Channel Erosion along the Deschutes River, Washington. Technical report prepared for Squaxin Island Tribe. Cramer, D Deschutes River Reach Scale Analysis and Habitat Survey. Prepared for the Thurston County Community and Environmental Programs and Thurston County Environmental Health Division. Prepared by the Thurston County Environmental Health Division. Ecology (Washington Department of Ecology) Deschutes River, Percival Creek, and Budd Inlet Tributaries Temperature, Fecal Coliform Bacteria, Dissolved Oxygen, ph, and Fine Sediment Total Maximum Daily Load, Water Quality Improvement Report and Implementation Plan DRAFT. Olympia, Washington. Ecology (Washington Department of Ecology) Deschutes River, Capitol Lake, and Budd Inlet Temperature, Fecal Coliform Bacteria, Dissolved Oxygen, ph, and Fine Sediment Total Maximum Daily Load Technical Report Water Quality Study Findings. Publication No Ecology Assessment of Surface Water / Groundwater Interactions and Associated Nutrient Fluxes in the Deschutes River and Percival Creek Watersheds, Thurston County. Publication No Olympia, WA. Fox, M. and S. Bolton A regional and geomorphic reference for quantities and volumes of instream wood in unmanaged forested basins of Washington State. North Am. J. Fish. Managem. 27: Fransen, B.R., P.A. Bisson, J.W. Ward, and R.E. Bilby Physical and biological constraints on summer rearing of juvenile coho salmon (Oncorhynchus kisutch) in small western Washington streams. In: Proceeding of the Coho Salmon Workshop, May 26-28, Nanaimo, BC. Haring, D. and J. Konovsky Salmonid habitat limiting factors: water resources inventory area 13. Final Report. Washington State Conservation Commission. Olympia, Washington. Healey, M.C Juvenile pacific salmon in estuaries: the life support system. Pp in V. S. Kennedy (ed.) Estuarine Comparisons. Academic Press, New York. LaMarche, J. and D.P. Lettenmaier Forest road effects on flood flows in the Deschutes River Basin, Washington. University of Washington Department of Civil Engineering. Water Resources Series Technical Report No Page 53

61 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Lestelle, L.C Coho Salmon (Oncorhynchus kisutch) Life History Patterns in the Pacific Northwest and California. Final Report. Prepared for U.S. Bureau of Reclamation Klamath Area Office. Poulsbo, WA. Lestelle, L.C., and S. Curtwright Queets River coho indicator stock study: 1987 smolt tagging and yield studies. Quinault Department of Natural Resources Annual Report for FY Contract No to the Northwest Indian Fisheries Commission, Taholah, WA. McCormick, S. D Ontogeny and evolution of salinity tolerance in anadromous salmonids: Hormones and heterochrony. Estuaries 17: Moser, M.L., A.F. Olsen and T.P. Quinn Riverine and Estuarine Migratory Behavior in Coho Salmon (Oncorhynchus kisutch) Smolts. Canadian Journal of Fisheries and Aquatic Sciences 48: Neher, T.D.H., A.E. Rosenberger, C.E. Zimmerman, C.M. Walker, and S.J. Baird Estuarine environments as rearing habitats for juvenile coho salmon in contrasting south-central Alaska Watersheds. Trans. Am. Fish. Soc. 142: NMFS (National Marine Fisheries Service) Final Recovery Plan for Central California Coast coho salmon Evolutionarily Significant Unit. National Marine Fisheries Service, Southwest Region, Santa Rosa, California. Pacific Groundwater Group Initial Watershed Assessment/Water Resources Inventory Area 13/Deschutes River Watershed. Department of Ecology, Lacey. Ecology Document Poole, G.C. and C.H. Berman An ecological perspective on instream temperature: natural heat dynamics and mechanisms of human caused thermal degradation. Environ. Mgmt. 27(6): Raines, M Mainstem Deschutes River Bank Erosion: 1991 to Prepared by the Northwest Indian Fisheries Commission. Prepared for Squaxin Island Tribe and Washington Dept. of Ecology, Shelton/Olympia, WA. Sandercock, F. K Life History of Coho Salmon (Oncorhynchus kisutch) in Pacific Salmon Life Histories. Groot, C. and Margolis, L. (ed.), Vancouver B.C.: UBC Press, pp Scheuerell, M.D., Hilborn, M.H. Ruckelshaus, K.K. Bartz, K.M. Lagueux, A.D. Haas, K. Rawson The Shiraz model: a tool for incorporating anthropogenic effects and fish habitat relationships in conservation planning. Can. J. Fish Aquat. Sci. 63: Seiler et al Schuett-Hames, D. et al Monitoring of the Upper Deschutes Watershed by the Squaxin Island Tribe. Schuett-Hames, D. and H. Flores Final Report: The Squaxin Island Tribe/Thurston County Streambed Characterization Contract; Squaxin Island Tribe. Shelton, WA. 9pp. Page 54

62 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN Schuett-Hames, D., H. Flores, and I. Child An Assessment of Salmonid Habitat and Water Quality for Streams in the Eld, Totten-Little Skookum, and Hammersley Inlet- Oakland Bay Watersheds in Southern Puget Sound, Washington Squaxin Island Tribe Natural Resources Department, Shelton. SPU (Seattle Public Utilities) and USACE (U.S. Army Corps of Engineers) Synthesis of Salmon Research and Monitoring Investigations Conducted in the Western Lake Washington Basin. Simenstad, C. A., K.L. Fresh, and E. O. Salo The role of Puget Sound and Washington Coastal Estuaries in the Life History of Pacific Salmon: An unappreciated function. Pp in V. S. Kennedy (ed.) Estuarine Comparisons. Academic Press, New York. 709 pp. Steltzner, S. and S. Haque Spurgeon Creek Habitat Survey. Squaxin Island Tribe. November 29, Steltzner, S. pers. comm. from Scott Steltzner, Squaxin Island Tribe, to Paul Schlenger, Confluence Environmental, re. results of wild coho acoustic tagging study in South Puget Sound. Steltzner, S. unpubl. data Coho rearing study. Squaxin Island Tribe. Sullivan, K., S.H. Duncan, P.A. Bisson, J.T. Heffner, J.W. Ward, R.E. Bilby and J.L. Nielsen A Summary Report of the Deschutes River Basin: Sediment, Flow, Temperature and Fish Habitat. Prepared for Weyerhaeuser Company, Tacoma, WA. Tabor, R. A., B. Footen, K L. Fresh, M. T. Celedonia, F. Mejia, D. L. Low, and L. Park Predation of juvenile Chinook salmon and other salmonids by smallmouth bass and largemouth bass in the Lake Washington basin. North American Journal of Fisheries Management 20: Taylor, K Deschutes River Off-channel habitat inventory. Final Report. Prepared by Kim Taylor, Water Resources Biologist with the Squaxin Island Tribe Natural Resources Department under contract with Thurston County. Thorsen, Gerald W. and Kurt L. Othberg Forest Slope Stability Pilot Project, Upper Deschutes River, Washington. Technical report (Open File Report 79-16) prepared for Washington State Department of Ecology by Washington Department of Natural Resources, Division of Geology and Earth Resources. Toth, S A road damage inventory for the upper Deschutes River Basin. Timber-Fish- Wildlife Report. TFW-SH Thurston County Deschutes Watershed Characterization. Prepared by the Thurston County Resource Stewardship Department and Geodata Center. Page 55

63 DESCHUTES RIVER COHO SALMON BIOLOGICAL RECOVERY PLAN USGS (United States Geological Survey) Streamflow records accessed on line on 9/14/2015 at and Vinson, M.R., and M.A. Baker Poor growth of rainbow trout fed New Zealand Mud Snails. North American Journal of Fisheries Management. 28: Watershed Sciences Aerial survey of the Deschutes River, Washington. Thermal infrared and color videography. Report to the Washington Dept. of Ecology. Corvallis, OR. WDF, WDW, and Western WA Treaty Indian Tribes Washington State Salmon and Steelhead Inventory Report. March WDFW Implications of Capitol Lake Management for Fish and Wildlife Final Report. Prepared for Capitol Lake Adaptive Management Program Steering Committee. Prepared by Hayes, M.P., T. Quinn, and T.L. Hicks. WDFW Implications of Capitol Lake Management for Fish and Wildlife Final Report. Prepared by M.P. Hayes, T. Quinn, and T.L. Hicks of WDFW. Prepared for Capitol Lake Adaptive Management Program Steering Committee. September 11, WDFW Deschutes Coho Recovery Goals. WDFW Salmon Conservation Reporting Engine (SCoRE) Interactive Map. WDFW Wild Coho Forecasts for Puget Sound, Washington Coast, and Lower Columbia. Prepared by Mara Zimmerman, WDFW Science Division, Fish Program. WDFW. unpublished data. Deschutes coho smolt and adult production and survival database. Provided by Pete Topping, WDFW on September 15, Weitkamp, L.A., T.C. Wainwright, G.J. Bryant, G.B. Milner, D.J. Teel, R.G. Kope, and R.S. Waples Status review of coho salmon from Washington, Oregon, and California. NOAA Technical Memorandum NMFS-NWFSC-24. Zillges, G Methodology for Determining Puget Sound Coho Escapement Goals, Escapement Estimates, 1977 Pre-Season Run Size Prediction and In-Season Run Assessment. State of Washington Department of Fisheries. Olympia, WA. Technical Report No. 28. Page 56

64

65 Appendix A Shiraz Model Methods

66 APPENDIX A SHIRAZ MODEL METHODS Prepared for: Squaxin Island Tribe Natural Resources Department Authored by: Confluence Environmental Company

67 TABLE OF CONTENTS 1 INTRODUCTION Project Area Overview Coho Salmon Population Overview METHODS FOR SHIRAZ MODEL DEVELOPMENT Model Inputs Describing Coho Life History and Watershed Distributions Model Inputs to Describe Habitat Quantity Rearing Area Spawning Area Model Inputs to Describe the Functional Quality of Habitat Peak Flows Low Flow Rate High Water Temperatures Fine Sediments Large Woody Debris (LWD) Habitat Parameters Considered But Not Used in Model Model Calibration MODEL CALIBRATION TO EMPIRICAL DATA REFERENCES List of Tables Table 1 Natural Origin Adult Coho Returns to the Deschutes River... 4 Table 2 SHIRAZ Model Assessment Reaches... 5 Table 3 Rearing Area in Each Assessment Reach... 7 Table 4 Spawning Area Calculation in Each Assessment Reach... 8 Table 5 Peak Flows Between December and March at Tumwater Falls (RM 2) on the Deschutes River Table 6 Functional Relationship Between Low Flows and Coho Fry Survival Table 7 Number of Days Between May 1 and October Each Year with Low Flows Below 33 cfs at the USGS Gage on the Deschutes River at Rainier ( ) Table 8 Functional Relationship Between Summer Water Temperatures and Coho Fry Survival Table 9 Number of Days that Daily Maximum Water Temperatures at 1000 Road Exceeded 16 Degrees Celsius Table 10 Functional Relationship Between the Percentage of Fine Sediments (Less than 0.85 mm in Diameter) in Substrate and Coho Egg Survival Table 11 Percentage of Fine Sediment in Each Assessment Reach Table 12 Percentile Distribution of the Quantity of LWD per 328 Feet Stream Length for the Western Washington Region Table 13 Functional Relationship Between LWD Quantities and Coho Fry Survival Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan i

68 TABLE OF CONTENTS Table 14 Percentage of River Length in Each Assessment Reach Meeting Established LWD Restoration Target List of Figures Figure 2 Relationship between Peak Annual Flows and Coho Egg to Smolt Survival in the Deschutes River... 9 Figure 3 Functional Relationship Between Peak Annual Flow Rates and Coho Egg to Fry Survival Figure 4 Functional Relationship Between Low Flows and Coho Fry Survival Figure 5 Functional Relationship Between High Water Temperatures and Coho Fry Survival Figure 6 Functional Relationship Between the Percentage of Fine Sediments (Less than 0.85 mm in Diameter) in Substrate and Coho Egg Survival Figure 7 Functional Relationship Between LWD Quantities and Coho Fry Survival Figure 8 Comparison of Predicted and Actual Numbers of Natural Origin Adult Coho Salmon Returning Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan ii

69 INTRODUCTION 1 INTRODUCTION The habitat based population simulation model SHIRAZ was applied as a tool to inform the 2015 Deschutes River Coho Salmon Recovery Plan. A SHIRAZ model version developed in 2008 (Anchor Environmental 2008) to support an earlier coho salmon analysis was updated for this analysis. The methods information presented in this Appendix is derived primarily from the Anchor Environmental (2008) report. Limited updates were made to the peak flow and low flow inputs between 2008 and Also updated is text describing summer water temperature inputs and calibration results. The basis of the SHIRAZ model is the Beverton Holt stock recruitment model (Beverton and Holt 1957). The SHIRAZ model applies information on habitat features influencing the productivity and capacity of the river for producing coho to estimate the number of coho surviving each life stage in spatially distinct Assessment Reaches. The model allows the user to input watershed data on habitat conditions, coho population distributions, and the functional relationships between habitat and coho production. Model outputs are provided as the number of coho surviving each defined life stage in each Assessment Reach defined by the user. In this way, variations in the predicted number of coho provide insight on the effects of variations in model input (e.g., restored habitat). This report describes the development of functional relationships between habitat conditions and coho production in the Deschutes River watershed, and the construction of a SHIRAZ model utilizing these function linkages to characterize coho salmon population dynamics. Functional relationships developed in Anchor Environmental (2008) were retained and applied in this updated analysis. 1.1 Project Area Overview The Deschutes River watershed in Thurston County, Washington, encompasses approximately 166 square miles. The river originates on Cougar Mountain (3,870 feet) in the Snoqualmie National Forest and flows in a northwesterly directions for 57 miles. The river empties into Capitol Lake then drains into Budd Inlet in south Puget Sound (Figure 1). Historically, a natural barrier at the mouth of the river prevented anadromous salmonids Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 1

70 INTRODUCTION from entering the river system. In 1951, the lower 2 miles of the river were impounded to create Capitol Lake in the City of Olympia. In 1954, a fish ladder was completed at the natural barrier (named Tumwater Falls) at the head of Capitol Lake. The fish ladder allowed anadromous salmonid populations to utilize the Deschutes River and its tributaries. The upper extent of anadromous salmonid distribution in the river is Deschutes Falls at river mile (RM) 41. Source of Figure: Anchor Environmental (2008) Much of the upper watershed occurs in the transient snow zone between 1,100 and 3,600 feet elevation (Haring and Konovsky 1999). Transient snow zones are areas where rain onsnow precipitation events are common. The lower 41 miles of drainage flow through a broad prairie type valley floor. Much of the middle upper and upper watershed is managed for timber harvest by the Weyerhaeuser Company. The middle portion of the watershed also supports open farmland interspersed with dense stands of mixed deciduous and coniferous growth (Haring and Konovsky 1999). The lower portion of the watershed is an urban growth management area where the river flows through the city of Olympia. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 2

71 INTRODUCTION 1.2 Coho Salmon Population Overview Coho salmon are not native to the Deschutes River. Hatchery raised coho from around Puget Sound (primarily Green River stock) were introduced to the river between the late 1940s and 1981 (WDF et al. 1993). Since 1981, there have been no coho releases into the Deschutes basin, although releases from nearby net pens are believed to provide low numbers of adult hatchery strays (WDF et al. 1993). Due to the absence of hatchery releases, the stock is sustained by natural production and strays. In 2002, the Washington Department of Fish and Wildlife (WDFW) rated the Deschutes River coho stock as critical because of a severe short term decline in adult wild return numbers between 1998 and Recent WDFW data indicate the continuation of low numbers of returns (WDFW 2007; Table 1). WDF et al. (1993) indicates that the natural escapement goal for the Deschutes River is 8,100 coho. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 3

72 INTRODUCTION Table 1 Natural Origin Adult Coho Returns to the Deschutes River Return Year Number of Natural Origin Adult Coho Returns , , , , , , , , , , , , , , , , Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 4

73 METHODS FOR SHIRAZ MODEL DEVELOPMENT 2 METHODS FOR SHIRAZ MODEL DEVELOPMENT The methods information presented in this Appendix is derived primarily from the Anchor Environmental (2008) report. Limited updates were made to the peak flow and low flow inputs between 2008 and Also updated is text describing summer water temperature inputs and calibration results. The SHIRAZ model characterizes coho salmon production by life stage for individual Assessment Reaches within the project area. In the Deschutes River watershed, seven Assessment Reaches were identified through consultation with the Squaxin Island Tribe based on coho utilization and location within the watershed, as described in Table 2. Table 2 SHIRAZ Model Assessment Reaches Assessment Reach Mainstem RM 2 to 10 Tributaries RM 2 to 31 Mainstem RM 10 to 17 Mainstem RM 17 to 25 Mainstem RM 25 to 31 Mainstem RM 31 to 41 Tributaries RM 31 to 41 Description This reach extends from the fish ladder at Tumwater Falls upstream to the confluence of Spurgeon Creek with the river. Spurgeon Creek is the largest creek in the lower river. Tributaries below RM 31 are generally not utilized by coho as spawning areas, but provide rearing habitat. Transition reach from lower to middle portion of project area. Middle portion of project area. Transition reach from middle to upper portion of project area. Upper reach of project area and upper extent of anadromous fish distribution due to presence of Deschutes Falls at RM 41. These tributaries provide the most utilized spawning areas in the watershed. Parameters used in the SHIRAZ model had to meet two criteria: 1) there needed to be a documented link between the parameter condition and coho production; and 2) Deschutes River watershed data had to be available for the parameter. The documented link could be in peer reviewed literature or unpublished gray literature. In considering data availability, no new data were collected for this investigation. The parameters that met these criteria were: Peak flows Low flows High water temperatures Fine sediments Large woody debris (LWD) Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 5

74 METHODS FOR SHIRAZ MODEL DEVELOPMENT Rearing area Spawning area 2.1 Model Inputs Describing Coho Life History and Watershed Distributions The model was constructed using a simplified coho life history in which all coho completed the cycle in 3 years; this life history pattern is typical of most coho populations (Sandercock 1991). That is, adults return and deposit eggs in the fall of year i, alevins emerge and freshwater rearing occurs in year i + 1, smolts outmigrate to the ocean in year i + 2, and the adults return to begin the cycle again in the fall of year i + 3. This assumption of little to no variability in the duration of freshwater and marine residency is a convention used in virtually all coho life models. It facilitates the tracking of three isolated cycle lines for the population. There is not an extensive amount of data to describe the spawning and rearing distributions of coho in the Deschutes River watershed. Models inputs for the spatial distributions of coho spawning and rearing in each of the assessment reaches were based on descriptive information in WDFW Salmon and Steelhead Stock Inventory maps (2002), Haring and Konovsky (1999), and Sullivan et al. (1988). For model simplification, it was assumed that there was no colonization of spawning reaches. That is, fish produced in a reach will return and spawn in the same reach. This was a reasonable assumption for investigating restoration effects on coho population size, particularly since the system is not considered habitat capacity limited. 2.2 Model Inputs to Describe Habitat Quantity Rearing Area A fundamental component of the Beverton Holt (1957) model upon which the SHIRAZ model is built is the carrying capacity of the environment. Coho rearing area in the mainstem of the Deschutes River was calculated as the area within the vegetated width of the river as well as any adjacent wetlands. The delineation of this area was performed by Seto (2007). Rearing area within each mainstem Assessment Reach was calculated by dividing the mainstem into the reaches and using ArcGIS calculation tools for area. Rearing area within the tributaries was calculated based on the coho rearing distribution depicted in Haring and Konovsky (1999) and the WDFW Salmon and Steelhead Stock Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 6

75 METHODS FOR SHIRAZ MODEL DEVELOPMENT Inventory maps (2002) and assuming a stream width of 16.4 feet. Rearing areas in each Assessment Reach are presented in Table 3. Table 3 Rearing Area in Each Assessment Reach Assessment Reach Rearing Area (square feet) Mainstem RM 2 to 10 2,844,082 Tributaries RM 2 to 31 3,507,320 Mainstem RM 10 to 17 2,177,817 Mainstem RM 17 to 25 2,737,875 Mainstem RM 25 to 31 2,128,586 Mainstem RM 31 to 41 3,361,505 Tributaries RM 31 to 41 3,468, Spawning Area Spawning area was calculated by adjusting the rearing area estimates by the percentage of the Assessment Reach with suitable spawning gravel. Suitable spawning substrate size for coho salmon ranges from 0.5 to 6 inches with less than 20 percent of the substrate smaller than 0.25 inches (Hassler 1987). WDFW also uses 0.5 to 6 inches as optimal spawning substrate sizes for salmon (WDFW and Ecology 2004). The percentage of stream segments within each mainstem Assessment Reach with suitable spawning substrate was calculated using data from the Cramer (1997) reach analysis for the mainstem. The percentages of stream segments within the Tributary RM 2 to 31 and RM 31 to 41 reaches with suitable spawning substrate were calculated using descriptive information provided in Haring and Konovsky (1999) and data from the Squaxin Island Tribe (1991), respectively. Cramer (1997) provided pebble counts at multiple stream segments (range 43 to 87) within each of the Assessment Reaches defined for this study. For each mainstem Assessment Reach, the percentage of the stream segment with greater than 50 percent of the substrate between 0.9 and 5 inches and less than 20 percent of the substrate smaller than 0.3 inches (the closest size bin categories to target sizes) was calculated. In the Tributaries RM 31 to 41 Assessment Reach, data from nine stream segments in four different tributaries were used to calculate the percentage of the stream segments with suitable spawning substrate sizes. Table 4 presents the rearing area, percentage of Assessment Reach with suitable spawning substrate, and calculated suitable spawning area in each Assessment Reach. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 7

76 METHODS FOR SHIRAZ MODEL DEVELOPMENT Table 4 Spawning Area Calculation in Each Assessment Reach Assessment Reach Rearing Area (square feet) Percentage of Reach with Suitable Spawning Substrate Spawning Area (square feet) Mainstem RM 2 to 10 2,844, ,522,121 Tributaries RM 2 to 31 3,507, ,507,205 Mainstem RM 10 to 17 2,177, ,177,830 Mainstem RM 17 to 25 2,737, ,737,887 Mainstem RM 25 to 31 2,128, ,128,595 Mainstem RM 31 to 41 3,361, ,361,515 Tributaries RM 31 to 41 3,468, ,469, Model Inputs to Describe the Functional Quality of Habitat This section describes the scientific rationale for including peak flows, low flows, high water temperatures, fine sediment loads, and LWD as factors affecting the functional quality of habitat in the Deschutes River watershed and, ultimately, coho production. This section also describes the identified functional relationship between the parameters and coho survival and the model inputs. A functional relationship used as a model input describes the changes in the proportion of coho surviving a selected life stage over a range of conditions for a parameter. Typically, the range varies from optimal (1.0) to suboptimal or even lethal (0.0). The proportion of coho surviving and the habitat condition linked to that proportion is user defined. For the Deschutes River model, functional relationships were identified based on peer reviewed and unpublished literature, as well as (in some cases) the interpretation of observational data from the watershed on habitat conditions and coho survival. Natural coho production data for the Deschutes River beginning with 1977 were available from WDFW. WDFW operates a smolt trap on the lower river and the adult fish ladder facility at Tumwater Falls (RM 2) Peak Flows As is typical of western Washington watersheds, the highest river flows in the Deschutes River occur during winter rain and early spring snowmelt events. Because coho spawn between November and January, their eggs incubate in the gravel during the period of highest flows. As a result, their eggs are vulnerable to scour during their incubation Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 8

77 METHODS FOR SHIRAZ MODEL DEVELOPMENT period. High rates of salmon egg and alevin mortality can occur due to scour or aggradation caused by high flows (McHenry et al. 1994). The functional relationship between peak annual flow rates and coho egg to smolt survival was developed based on data from the U.S. Geological Survey (USGS) gage on the Deschutes River at Rainier ( ). A regression between daily peak flows and the coho egg to smolt survival documented by WDFW between 1987 and 2005 explained 35 percent of the variability (r 2 = 0.35; Figure 2). The functional relationship developed followed approximately the same shape as the logarithmic regression (Figure 3). Egg-to-Smolt Survival 9% 8% 7% 6% 5% 4% 3% 2% 1% 0% 0 2,000 4,000 6,000 8,000 10,000 Peak Flow (cubic feet per second) Sources: WDFW egg to smolt survival data and USGS flow data at gage Note: Line depicts logarithmic regression line describing relationship (r2 = 0.35) Figure 2 Relationship between Peak Annual Flows and Coho Egg-to-Smolt Survival in the Deschutes River Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 9

78 METHODS FOR SHIRAZ MODEL DEVELOPMENT Coho Fry Survival ,000 4,000 6,000 8,000 10,000 Peak Flow (cubic feet per second) Figure 3 Functional Relationship Between Peak Annual Flow Rates and Coho Egg-to-Fry Survival Peak flow data from the USGS gage on the Deschutes River at Rainier ( ) are presented in Table 5. For years in which no data were available, the peak flow input for the model was adjusted to improve the calibration of the overall model to observed adult returns (i.e., reduce the difference between predicted returns and actual returns). For future years (2006 to 2050), the average of the years with data was used in the model. This average daily peak flow in a water year was 3,355 cubic feet per second (cfs). Table 5 Peak Flows Between December and March at Tumwater Falls (RM 2) on the Deschutes River Water Year Peak Flow (cfs) , No data , , No data 1984 No data 1985 No data 1986 No data 1987 No data , , , ,980 Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 10

79 METHODS FOR SHIRAZ MODEL DEVELOPMENT , , , , , , , , , , , , , , , , , , , , , ,510 Note: In years listed as having no data, USGS did not have a calculated peak flow available Low Flow Rate In western Washington watersheds, the lowest flows of the year typically occur during mid to late summer and early fall. Analyses of historic western Washington data from as far back as 1935 have shown a positive relationship between summer streamflow and the natural production of coho (Smoker 1955 and Mathews and Olson 1980). That is, higher summer streamflows during the oversummer rearing of coho in year i tend to result in higher numbers of adult coho in year i + 2. This effect on coho can be due to low flows limiting juvenile coho access to rearing areas, increased high water temperatures, and decreased dissolved oxygen levels. For adult coho, low flows can limit upstream migration and access to tributaries for spawning. In this way, low flows can limit spawning areas and concentrate redds in areas which may be more vulnerable to scour during high flow events during egg incubation. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 11

80 METHODS FOR SHIRAZ MODEL DEVELOPMENT The functional relationship between low flows and coho survival was developed based on the relationship between WDFW smolt data and low flow data from the USGS gage on the Deschutes River at Rainier ( ). Statistical analysis identified a modest negative relationship (r 2 = 0.07) between the number of days between May 1 and October 31 with low flows below 33 cfs and the number of outmigrating smolts the following year. Available data were from 1979 to The functional relationship developed followed approximately the same shape as the logarithmic regression (Table 6 and Figure 4). Table 6 Functional Relationship Between Low Flows and Coho Fry Survival Number of Days in a Year with Proportion of Coho Fry Low Flow Rates Below 33 cfs Survival Coho Survival Number of Days with Flows Below 33 cfs Figure 4 Functional Relationship Between Low Flows and Coho Fry Survival Low flow data in the form of the number of days each year between May 1 and October 31 with flows below 33 cfs recorded at the USGS gage on the Deschutes River at Rainier ( ) are presented in Table 7. For previous years in which no data were available, 1977 and 1978, the average number of days with flows below 33 cfs recorded during the Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 12

81 METHODS FOR SHIRAZ MODEL DEVELOPMENT first 6 years of the dataset was used. In this way, for years 1977 and 1978, a low flow value of 2 days was used in the model. For future years, the average of the years with data was used in the model. This average number of days with flows below 33 cfs was 64 days. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 13

82 METHODS FOR SHIRAZ MODEL DEVELOPMENT Table 7 Number of Days Between May 1 and October Each Year with Low Flows Below 33 cfs at the USGS Gage on the Deschutes River at Rainier ( ) Number of Days Between May 1 and October 31 Each Year with Year Low Flows Below 33 cfs Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 14

83 METHODS FOR SHIRAZ MODEL DEVELOPMENT High Water Temperatures Water temperatures are a critical element of habitat quality for salmonids, because they impact salmonid survival, growth, and fitness. Richter and Kolmes (2004) identified 12 to 14 degrees Celsius as the preferred range for rearing juvenile salmon. Brett (1952) documented optimum growth between 12 and 14 degrees Celsius. Brett (1971) reported optimal physiological conditions at less than 15 degrees Celsius, and in another study, Brett (1952) documented marked avoidance of temperatures above 15 degrees Celsius. Frissell (1992) reported field studies findings that coho, cutthroat trout (Oncorhynchus clarkii), and yearling steelhead (O. mykiss) rearing densities decreased linearly as temperatures exceeded 17 degrees Celsius. Frissell (1992) also found that coho salmon juveniles were absent in waters that reached 21 to 23 degrees Celsius, except where thermal refugia were available. The Water Quality Standards for Surface Waters of the State of Washington (Chapter Washington Administrative Code [WAC]) set the upper temperature threshold in the Deschutes River watershed at 16 degrees Celsius for those areas upstream of the tributary to Offut Lake (RM 15). Downstream from the tributary to Offut Lake, the upper temperature threshold is 17.5 degrees Celsius. The temperature threshold for analysis in the Deschutes River was defined as 16 degrees Celsius. Data from a temperature gage operated by Weyerhaeuser at 1000 Road (RM 37) were used for the analysis because this gage provides the most complete dataset over the period of analysis. The functional relationship between summer daily maximum water temperatures and coho survival was developed based on the relationship between WDFW smolt data and the 1000 Road water temperature data. A long term dataset of water temperatures at 1000 Road between May 1 and September 30 was available. This 153 day period was the basis of the statistical analysis and subsequent functional relationship development. Statistical analysis identified a negative relationship between the number of days each year with maximum water temperatures at 1000 Road exceeding 16 degrees Celsius and egg to smolt survival among smolts outmigrating the following year (r 2 = 0.10). Available data were from 1981 to 2004, and the number of days with maximum water Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 15

84 METHODS FOR SHIRAZ MODEL DEVELOPMENT temperatures at 1000 Road exceeding 16 degrees Celsius ranged from 32 to 94. The regression slope describing this relationship was used to describe the functional relationship between maximum water temperatures and coho fry survival for years with between 30 and 153 days with maximum water temperatures greater than 16 degrees Celsius (Table 8 and Figure 5). Since the regression analysis did not have data available for fewer days with maximum water temperatures exceeding 16 degrees Celsius, best professional judgment was applied to describe the diminished coho fry survival expected in such years. Table 8 Functional Relationship Between Summer Water Temperatures and Coho Fry Survival Number of Days in a Year with Daily Maximum Temperatures Greater Than 16 Degrees Proportion of Coho Fry Celsius Survival Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 16

85 METHODS FOR SHIRAZ MODEL DEVELOPMENT Coho Fry Survival Number of Days with Daily Maximum Temperatures Greater Than 16 Degrees Celsius Figure 5 Functional Relationship Between High Water Temperatures and Coho Fry Survival Summer water temperatures from 1000 Road were used in the analysis and were defined on an annual basis. The number of days exceeding 16 degrees Celsius during each year with available data is presented in Table 9. For years in which no data were available, the average of the years with data was used in the model. This average was 57 days per year. Table 9 Number of Days that Daily Maximum Water Temperatures at 1000 Road Exceeded 16 Degrees Celsius Year Number of Days Year Number of Days Year Number of Days 1980 No data No data No data Note: In years listed as having no data, an incomplete record of summer water temperatures was available. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 17

86 METHODS FOR SHIRAZ MODEL DEVELOPMENT Fine Sediments For the purposes of this analysis, fine sediments were defined as sediment particles less than 0.85 millimeter (mm) in diameter. Field and laboratory studies have documented that higher percentages of fine sediments reduce salmon egg survival (Chapman 1988). McNeil and Ahnell (1964) found that fine sediments of less than 0.85 mm had the highest impact on salmonid spawning success. Several authors have documented that salmon egg survival decreases markedly when more than 10 percent fine sediment is present in redds (Koski 1966; Cedarholm et al. 1981; Tappel and Bjornn 1983). Other studies or protocols use slightly higher fine sediment percentages (e.g., Timber Fish and Wildlife Watershed Analysis Rating System uses 12 percent fine sediment as the threshold for decreased survival; McHenry et al. [1994] identified 13 percent fine sediment as the threshold). Based on information on decreased survival with increasing percentages of fine sediments, a functional relationship was defined. The functional relationship describes the trend in the proportion of egg to fry survival based on percentage of fine sediments present (Table 10 and Figure 6). Table 10 Functional Relationship Between the Percentage of Fine Sediments (Less than 0.85 mm in Diameter) in Substrate and Coho Egg Survival Percent Fines in Substrate Proportion of Coho Egg Survival Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 18

87 METHODS FOR SHIRAZ MODEL DEVELOPMENT Proportion of Eggs Surviving Percent Fines Figure 6 Functional Relationship Between the Percentage of Fine Sediments (Less than 0.85 mm in Diameter) in Substrate and Coho Egg Survival The information sources for fine sediment data in the Deschutes River Assessment Reaches were fine sediment data for the mainstem river collected by Konovsky and Puhn (2005) and tributary data collected by Schuett Hames and Flores (1994) as reported in Haring and Konovsky (1999). The dataset produced by Konovsky and Puhn (2005) included measurements of the percentage of fine sediments for one study site within each of the mainstem Assessment Reaches defined for this analysis. The fine sediment percentage in the Tributaries RM 2 to 31 Assessment Reach was an average of the Konovsky and Puhn (2005) data in the five mainstem Assessment Reaches. The fine sediment percentage in the Tributaries RM 31 to 41 Assessment Reach was the average of data from five tributaries in the Schuett Hames and Flores (1994) study. The fine sediment data input to the model are presented in Table 11. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 19

88 METHODS FOR SHIRAZ MODEL DEVELOPMENT Table 11 Percentage of Fine Sediment in Each Assessment Reach Assessment Reach Percentage of Fine Sediment Mainstem RM 2 to Tributaries RM 2 to Mainstem RM 10 to Mainstem RM 17 to Mainstem RM 25 to Mainstem RM 31 to Tributaries RM 31 to Large Woody Debris (LWD) LWD is defined as a log that is at least 7 feet long with a diameter of at least 4 inches. LWD provides habitat structure that juvenile coho use and is an important factor in pool formation (Bisson et al. 1987). Pools help retain organic matter and detritus and increase the amount of slow water habitat available (Sedell et al. 1988). LWD is used as an indicator of pool density, but is considered less subjective than available datasets that provided some estimation of pool abundance. LWD both within and outside the low flow channel may play a crucial role in helping fish survive winter high flow conditions (Reeves et al. 1991). LWD, including rootwads, can provide slow water areas during periods of high flow. Shirvell (1990) reported that 99 percent of all coho fry occupied positions immediately downstream of rootwads during periods of low, average, and high flows. The use of LWD rather than pool data in the model was based on the fact that the available LWD information appeared to be more consistent and complete than the datasets on pools. Both parameters were not utilized in the model because they are typically highly correlated. The functional relationship between LWD quantities and coho production was developed based on LWD quantity data presented in Fox and Bolton (2007) for three sizes of river and stream systems throughout western Washington (Table 12). Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 20

89 METHODS FOR SHIRAZ MODEL DEVELOPMENT Table 12 Percentile Distribution of the Quantity of LWD per 328 Feet Stream Length for the Western Washington Region Bankfull Width Median 25th Percentile 75th Percentile Less than 20 feet to 98 feet Greater than 98 to 328 feet Source: Fox and Bolton (2007) In this analysis, the central 50 percent of these data (i.e., as bounded by the 25th and 75th percentiles) was established as a reasonable target for habitat restoration in the Deschutes River. The intermediate bankfull width category (20 to 98 feet) describes the mainstem Assessment Reaches. The smallest bankfull width category (less than 20 feet) describes the tributary Assessment Reaches. The functional relationship was based on the percentage of each Assessment Reach that contains LWD quantities per 328 feet at or above the 25th percentile. For the mainstem, the minimum LWD requirement to count as favorable for coho was 29 or more pieces per 328 feet stream length. In tributaries, the minimum LWD requirement was 26 pieces per 328 feet stream length. The literature describing the importance of LWD for salmon does not provide clear documentation of the survival or productivity impacts that result from little or no LWD availability in river systems. The functional relationship was developed based on best professional judgment of the role of LWD in the survival of fry to the over wintering life stage (Table 13 and Figure 7). Table 13 Functional Relationship Between LWD Quantities and Coho Fry Survival Percent of Reach with Good or Fair LWD Conditions Proportion of Coho Fry to Over-winter Survival Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 21

90 METHODS FOR SHIRAZ MODEL DEVELOPMENT 1.0 Proportion of Fry Surviving Percentage of Reaches with More Than 25th Percentile of LWD Quantities Per 328 Feet Stream Length Figure 7 Functional Relationship Between LWD Quantities and Coho Fry Survival Data on the quantities and distribution of LWD in the Deschutes River Assessment Reaches were obtained from a mainstem reach scale survey conducted by Cramer (1997) and tributary data collected by the Squaxin Island Tribe (1991). Cramer (1997) provided LWD counts at multiple stream segments (range 43 to 87) within each of the Assessment Reaches defined for this study. For each mainstem Assessment Reach, the percentage of the stream segments with LWD quantities per 328 feet in excess of the 25th percentile were calculated. The percentage of the streams in the Tributaries RM 2 to 31 Assessment Reach with LWD quantities per 328 feet in excess of the 25th percentile was calculated as the average of the mainstem Assessment Reach results. In the Tributaries RM 31 to 41 Assessment Reach, data from nine stream segments in four different tributaries was used to calculate the percentage of the stream segments with LWD quantities per 328 feet in excess of the 25th percentile. The LWD data input to the model are presented in Table 14. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 22

91 METHODS FOR SHIRAZ MODEL DEVELOPMENT Table 14 Percentage of River Length in Each Assessment Reach Meeting Established LWD Restoration Target Percentage of River Length Meeting Established LWD Assessment Reach Restoration Target a Mainstem RM 2 to 10 2 Tributaries RM 2 to 31 1 Mainstem RM 10 to 17 0 Mainstem RM 17 to 25 0 Mainstem RM 25 to 31 2 Mainstem RM 31 to 41 0 Tributaries RM 31 to Note: LWD restoration target based on 25th percentile of LWD quantity data for river size presented in Fox and Bolton (2007) and shown in Table Habitat Parameters Considered But Not Used in Model A myriad of ecological parameters could potentially be used to describe the functional quality of the habitat for coho. The lack of a clear, defensible link between a parameter and coho production and/or the absence of an adequate dataset excludes other parameters from being included in this version of the model. Three parameters given some consideration but ultimately not included in the model were off channel rearing habitat availability, pool availability, and total nitrogen levels. The importance of off channel rearing habitat to the life cycle of coho has been well documented, but the parameter was not explicitly included in the model because of a lack of data on off channel habitat availability in the watershed. Instead, the estimation of rearing habitat included the area contained in adjacent wetlands in order to generally describe off channel habitat availability. An indicator of pool availability was not included because it is correlated to LWD, which is included in the model, and the estimation of pool availability in available datasets was considered to be a more subjective measure than the available LWD counts. Insufficient data on nitrogen levels in the watershed to support inclusion in the model prevented further consideration of this parameter. 2.5 Model Calibration Model calibration is the process of iteratively refining model inputs in an effort to minimize the difference between predicted and actual outcomes. For this model, the WDFW coho production data (WDFW unpubl. data) provides an excellent long term dataset comprised Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 23

92 METHODS FOR SHIRAZ MODEL DEVELOPMENT of empirical observations. Model predictions were refined by adjusting the peak flow entries in those years for which no data were available (1979 and 1982 through 1986). Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 24

93 RECOMMENDATIONS 3 MODEL CALIBRATION TO EMPIRICAL DATA The model was calibrated to the number of natural origin coho salmon returning as adults between 1980 and 2006 (WDFW unpubl. data). The resulting model accurately estimated the number of fish returning in a given year and the general trend of returns over the period of comparison (Figure 8). However, the recent rebound in natural origin coho production is underestimated by the model, so baseline numbers used in model scenarios to predict coho production responses to improvements in freshwater survival through habitat restoration may underestimate actual numbers but still accurately predict population trends. Overall, the results suggest a high degree of confidence in the model s ability to characterize subsequent changes to the size of the Deschutes River coho population due to changes in the habitat parameters and marine survival conditions. Figure 8 Comparison of Predicted and Actual Numbers of Natural Origin Adult Coho Salmon Returning Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 25

94 REFERENCES 4 REFERENCES Anchor (Anchor Environmental, LLC) Final Deschutes River Watershed Recovery Plan: Effects of Watershed Habitat Conditions on Coho Salmon Production. Prepared for Squaxin Island Tribe Natural Resources Department, Shelton, WA. Beverton, R.J.H. and S.J. Holt On the dynamics of exploited fish populations. Fisheries Investment Series 2, Volume 19. U.K. Ministry of Agriculture and Fisheries, London. Bisson, P. A., R. E. Bilby, M. D. Bryant, C. A. Dolloff, G. B. Grette, R. A. House, M. L. Murphy, K. V. Koski, and J. R. Sedell Large woody debris in forested streams in the Pacific Northwest: past, present and future. Pages in E.O. Salo and T.W. Cundy, editors. Streamside Management Forestry and Fishery Interactions. Univ. of Wash., Institute for Forest Resources, Contribution 57, Seattle, WA. Brett, J.R Temperature tolerance in young Pacific salmon, genus Oncorhynchus. J. Fish. Res. Board of Canada. 9(6): Brett, J.R Energetic responses of salmon to temperature. A study of some thermal relations in the physiology and freshwater ecology of sockeye salmon (Oncorhynchus nerka). Am. Zool. 11: Cedarholm, C.J., L.M. Reid, and E.O. Salo Cumulative effects of logging road sediment on salmonid populations of the Clearwater River, Jefferson County, Washington. Pages in Proceedings of Conference on Salmon Spawning Gravel: A Renewable Resource in the Pacific Northwest? Report 19. Wash. State University, Water Research Center, Pullman, WA. Chapman, D.W Critical Review of Variables Used to Define Effects of Fines in Redds of Large Salmonids. Transactions of the American Fisheries Society 117: Cramer, D Deschutes River Reach Scale Analysis and Habitat Survey. Prepared for the Thurston County Community and Environmental Programs and Thurston County Environmental Health Division. Prepared by the Thurston County Environmental Health Division. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 26

95 REFERENCES Fox, M. and S. Bolton A regional and geomorphic reference for quantities and volumes of instream wood in unmanaged forested basins of Washington State. North Am. J. Fish. Managem. 27: Frissell, C.A Cumulative effects of land use on salmonid habitat on southwest Oregon streams. Ph.D. thesis, Oregon State University, Corvalis, OR. As cited in Haring, D. and J. Konovsky Salmonid habitat limiting factors: water resources inventory area 13. Final Report. Washington State Conservation Commission. Olympia, Washington. Hassler, T. J Species Profiles: Life Histories and Environmental Requirements of Coast Fishes and Invertebrates (Pacific Southwest) Coho Salmon. U.S. Fish Wild. Serv. Bio. Rep. 82(11.70). U.S. Army Corps of Engineers. Konovsky, J. and J. Puhn Trends in spawning gravel fine sediment levels Deschutes River, Washington. Squaxin Island Tribe, Shelton, Washington. Koski, K.V The survival of coho salmon (Oncorhynchus kisutch) from egg deposition to emergence in three Oregon coastal streams. Masterʹs thesis, Oregon State University. 98 pp. Mathews, S.B. and F.W. Olson Factors affecting Puget Sound coho salmon (Oncorhynchus kisutch). Can. J. Fish. Aquat. Sci. 37: McHenry, M.L., D.C. Morrill, and E. Currence Spawning Gravel Quality, Watershed Characteristics and Early Life History Survival of Coho Salmon and Steelhead in Five North Olympic Peninsula Watersheds. Lower Elwha SʹKlallam Tribe, Port Angeles, WA. and Makah Tribe, Neah Bay, WA. McNeil, W.J. and W.H. Ahnell Success of Pink Spawning Relative to Size of Spawning Bed Material. U.S. Fish and Wildlife Service, Special Scientific Report Fisheries No Washington, D.C. 17 pp. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 27

96 REFERENCES Reeves, G.H., J.D. Hall, T.D. Roelofs, T.L. Hickman, and C.O. Baker Rehabilitating and modifying stream habitats. Pages in W.R. Meehan, editor. Influences of Forest and Rangeland Management on Salmonid Fishes and Their Habitats. American Fisheries Society, Special Publication 19, Bethesda, MD. Richter, A. and S.A. Kolmes Maximum temperature limits for Chinook, Coho, and chum salmon, and steelhead trout in the Pacific Northwest. Reviews in Fisheries Science 13(1): Sandercock, F.K Life History of Coho Salmon. In Groot, C. and L. Margolis (Eds.). Pacific Salmon Life Histories. UBC Press, Vancouver. 564 p. Schuett Hames, D. and H. Flores Final Report: The Squaxin Island Tribe/Thurston County Streambed Characterization Contract; Squaxin Island Tribe. Shelton, WA. 9pp. Sedell, J. R., P. A. Bisson, E J. Swanson, and S. V. Gregory What we know about large trees that fall into streams and rivers. Pages in C. Maser, R. F. Tarrant, J. M. Trappe, and J. E Franklin, From the forest to the sea: a story of fallen trees. U.S. Forest Service General Technical Report PNW GTR 229. Seto, C GIS polygon shapefile of mainstem Deschutes River area within the vegetated width between river mile 2 and the upper end of the anadromous zone (river mile 41) including wetlands. Shapefile created by Colleen Seto of the Squaxin Island Tribe Natural Resources Department. Shirvell, C.S Role of instream rootwads as juvenile coho salmon (Oncorhynchus kisutch) and steelhead trout (O. mykiss) cover habitat under varying streamflows. Canadian Journal of Fisheries and Aquatic Sciences 47: Smoker, W.A Effects of stream flow on silver salmon production in western Washington. Ph.D. dissertation, Univ. Washington, Seattle, WA. 175 p. Squaxin Island Tribe Monitoring of the Upper Deschutes Watershed. Compiled in cooperation with the Thurston County Office of Water Quality. Funded by the Washington Centennial Clean Water Fund. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 28

97 REFERENCES Sullivan, K., S.H. Duncan, P.A. Bisson, J.T. Heffner, J.W. Ward, R.E. Bilby, and J.L. Nelson A Summary Report of the Deschutes Basin: Sediment Flow, Temperature, and Fish Habitat. Prepared by the Weyerhaeuser Company. Paper No /87/1. Tappel, P.D., and T.C. Bjornn A new method of relating size of spawning gravel to salmonid embryo survival. North American Journal of Fisheries Management 3: Taylor, K Deschutes River Off channel habitat inventory. Final Report. Prepared by Kim Taylor, Water Resources Biologist with the Squaxin Island Tribe Natural Resources Department under contract with Thurston County. Washington Department of Fish and Wildlife (WDFW) Washington State Salmon and Steelhead Stock Inventory. Prepared by Washington Department of Fish and Wildlife, Olympia, Washington. Available at SalmonScape at: WDFW. unpublished data. Deschutes coho smolt and adult production and survival database. Provided by Pete Topping, WDFW on September 15, WDFW and Washington State Department of Ecology (Ecology) Instream Flow Study Guidelines: technical and habitat suitability issues. Updated, April 5, Prepared by Washington Department of Fish and Wildlife and Washington Department of Ecology (Ecology). Available at Washington Department of Fisheries (WDF), Washington Department of Wildlife (WDW), and Western Washington Treaty Indian Tribes (WWTIT) Washington State salmon and steelhead stock inventory (SASSI). Wash. Dep. Fish Wildl., Olympia, 212 p. + 5 regional volumes. Appendix A SHIRAZ Model Methods Deschutes River Coho Salmon Recovery Plan 29

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