PNWD-4325

Habitat Quality and Fish Species Composition/Abundance at Selected Shallow-Water Locations in the Lower Snake River Reservoirs, 2010–2011

Final Report

EV Arntzen DD Dauble KJ Klett B Ben James BL Miller AT Scholz RP Mueller MC Paluch RA Harnish D Sontag MA Nabelek G Lester

Battelle Pacific Northwest Division Richland, Washington 99352

Prepared for U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington under Biological Services Contract W912EF-08-D-0004 Delivery Order 0005

January 2012

PNWD-4325

Habitat Quality and Fish Species Composition/Abundance at Selected Shallow-Water Locations in the Lower Snake River Reservoirs, 2010–2011

Final Report

EV Arntzen1 DD Dauble2 KJ Klett1 B Ben James3 BL Miller1 AT Scholz4 RP Mueller1 MC Paluch4 RA Harnish1 D Sontag4 MA Nabelek1 G Lester5

Battelle Pacific Northwest Division Richland, Washington 99352

Prepared for U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington under Biological Services Contract W912EF-08-D-0004 Delivery Order 0005

January 2012

______1 Battelle–Pacific Northwest Division, Richland, Washington. 2 Washington State University Tri-Cities, Richland, Washington. 3 Cascade Aquatics LLC, Ellensburg, Washington. 4 Eastern Washington University, Cheney, Washington. 5 EcoAnalysts, Inc., Moscow, Idaho.

Final Report

Summary

The Walla Walla District of the U.S. Army Corps of Engineers (USACE) has begun development of a Programmatic Sediment Management Plan to manage dredged material in the lower Snake River. During 2008, research evaluating the potential use of dredged sediments to create additional shallow-water salmonid rearing habitat was expanded from Lower Granite Reservoir to include all four reservoirs on the lower Snake River. The primary goal of the study reported here was to characterize existing habitats on the lower Snake River having features suitable for rearing salmonids so that dredged material could be used to create similar habitat.

Twenty-four locations throughout the lower Snake River were studied from November 2010 through September 2011, to assess habitat quality and biological integrity, with an emphasis on seasonal variability. Fish species composition and abundance were determined using beach seines, electrofishing, and snorkeling, with a focus on naturally produced subyearling fall Chinook salmon (Oncorhynchus tshawytscha) as an indicator of existing suitable habitat. In an attempt to determine the presence or absence of larval Pacific lamprey (Lampetra tridentata) in deepwater habitat (>1 m), a submersible electrofishing sled coupled to an optical camera was developed. Trophic levels were examined by collecting phytoplankton, periphyton, zooplankton, and macroinvertebrates on a seasonal basis to characterize the biological productivity of sample sites. Water quality was evaluated using temperature, dissolved oxygen, pH, and specific conductance. Sediment samples were collected to determine grain- size distribution and organic content.

Fish sampling yielded 18,676 fish representing 31 different species. A total of 2,648 Chinook salmon were captured; many were found in the region surrounding Lower Granite Dam. Seining produced more ocean-type Chinook salmon subyearlings, while electrofishing produced more Chinook salmon yearlings, although they were generally found at the same sites. The most frequently captured predator species were northern pikeminnow (Ptychocheilus oregonensis; n = 97) and smallmouth bass (Micropterus dolomieu; n = 264), which were seen throughout all reservoirs. One bull trout (Salvelinus confluentus) was sampled in April at the mouth of the Tucannon River. This individual was most likely a member of the Tucannon River population, some of which are thought to overwinter in the main-stem Snake River. No larval or adult lamprey were observed during any field sampling (July–September 2011).

Indicators of biological productivity, including zooplankton density, as well as mean phytoplankton biomass and chlorophyll a content, peaked during spring and were lowest during fall and winter in the Snake River reservoirs. Both mean phytoplankton density and periphyton biomass were lowest during fall and winter.

Macroinvertebrate family diversity was highest at sites within Lower Granite Reservoir. Relative abundances of orders that are important food sources for juvenile salmonids (i.e., Diptera, Ephemeroptera, Plecoptera, and Trichoptera, or DEPT) generally ranged from 60% to 90% throughout the lower Snake River. The mean relative abundance of DEPT was significantly higher at Lower Monumental and Lower Granite sites than Ice Harbor sites and was greatest along free-flowing reaches (i.e., Asotin), where the gravel substrate likely provided ample interstices, i.e., refugia for the insects. Mean biomass of DEPT was lowest at Little Goose sites. Mean spring (April–June) DEPT biomass, per transect, was greater on angular colluvium substrates than on alluvium.

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Water quality was similar among sites and generally favorable for salmonid rearing and growth, although summer temperatures frequently exceeded 20°C, approaching 24°C in Lower Granite Reservoir. Significant depth gradation and diel fluctuation of temperature (up to 7°C) was observed in Lower Granite Reservoir and at New York Island within Little Goose Reservoir during the summer. Depth gradation of temperature was also observed at Devil’s Bench. Dissolved oxygen levels ranged from 85% to 115% and were supersaturated and more variable during spring spill. pH ranged from 6.5 to 8 and was also more variable during spring spill.

Snake River sediments were composed of silt, sand, and gravel, with sand (0.063–2 mm) the most abundant size class measured. Our study and previous research specific to the lower Snake River suggest that subyearling Chinook salmon prefer sand substrates over gravel. Nonparametric multiplicative regression (NPMR) analyses revealed strong relationships between juvenile Chinook salmon, low amounts of gravel, and high amounts of DEPT biomass. NPMR analysis also showed that Chinook salmon used all size classes of sand (0.063 mm–2 mm) but presence was negatively associated with silt. No relationship was found between predator locations and underlying sediment size class. Previous research has shown that biomass and species richness of benthic macroinvertebrates is maximized when the percentage organic content of sediments remains below 6%. Organic content of Snake River locations ranged from 0.66% to 8.7% throughout the study, exceeding 6% during the spring at Knoxway Bench Upper (8.7%), Knoxway Bay Upper (6.6%), and Offield Landing Lower (6.4%). Sediment grain-size distribution showed that locations dominated by silt (<0.063 mm) were within embayments, areas where tributaries entered reservoirs, or locations within Ice Harbor Reservoir. The Asotin site and main-stem locations with steep lateral bed slopes had the highest percentage of gravel (>2 mm). Backwater and main-stem areas with gradual lateral bed slopes had significantly less gravel than Asotin and areas with steep lateral bed slopes.

Highest numbers (83% of total) juvenile Chinook salmon were located within Lower Granite Reservoir and its tailrace, at sites characterized by a gradual lateral bed slope. In addition, the relative abundance of macroinvertebrate taxa (DEPT) preyed upon by juvenile Chinook salmon was also relatively high in the vicinity of Lower Granite Dam, further suggesting that if suitable locations can be identified for the creation of additional shallow-water habitat in this vicinity, juvenile salmonid rearing habitat can be increased there. Sand (0.063–2 mm) was preferred by juvenile Chinook salmon to gravel and silt, further supporting the potential utility of sediment management activities that create additional shallow-water habitat. Sites upstream of rkm 120 (near New York Island), sediment distribution of sand, and DEPT biomass all were positively correlated with presence of subyearling Chinook salmon. There was little indication that newly created shallow-water habitat would substantially increase salmonid predation by smallmouth bass (Micropterus dolomieu)—the most frequently captured predator during our study—which were found to have diets consisting of less than 6% juvenile Chinook salmon by weight. No lamprey were found at study sites where sediment management activities could potentially be conducted. Water quality was generally favorable for juvenile salmonid rearing, although temperatures were relatively low during summer 2011 due to unusually high river discharge. Organisms at all trophic levels were generally much more prolific in spring and summer than in winter, suggesting that sediment management activities should take place during the winter.

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Acknowledgments

Assistance for this project was provided by many different individuals and agencies, to whom we owe our gratitude. Funding for this work was provided by the U.S. Army Corps of Engineers (USACE), Walla Walla District. Special assistance from the USACE was provided by Karen Zelch, Adam Daniel, Chris Pinney, Ann Setter, Richard Turner, and David Trachtenbarg. Shanda McGraw, Dawn Hamilton, Pat Barrett, John Pfeiffer, Matt Hill, and Charles Ingwell (EcoAnalysts, Inc.) helped process zooplankton, phytoplankton, and periphyton samples in the laboratory. Austin Huff (Cascade Aquatics LLC) assisted with beach seining, snorkeling, sediment sample collection, and data processing. We thank Geoff McMichael (Battelle) for his valuable advice throughout the project. Scott Titzler (Battelle) assisted with the design and deployment of water quality monitoring equipment. Battelle staff, including Lori Ortega, Graysen Squeochs, Ricardo Walker, and Kris Hand, assisted with beach seining efforts and searches for juvenile lamprey. Andrea LeBarge (Battelle) photographed representative macroinvertebrate specimens. Andrea Currie (Battelle) provided editorial assistance.

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Abbreviations and Acronyms

AFDM ash-free dry mass cm centimeter(s) CPUE catch-per-unit-effort d day(s) DEPT Diptera, Ephemeroptera, Plecoptera, and Trichoptera DGPS differential Global Positioning System DMMP/EIS Dredged Material Management Plan/Environmental Impact Statement DO dissolved oxygen EPA U.S. Environmental Protection Agency EPT Ephemeroptera, Plecoptera, and Trichoptera h hour(s) m meter(s) mm millimeter(s) MS-222 tricaine methanesulfonate (CASRN)

NaHCO3 sodium bicarbonate NPMR nonparametric multiplicative regression NTU nephelometric turbidity unit(s) rkm river kilometer(s) s second(s) TDG total dissolved gas TMDL total maximum daily load USACE U.S. Army Corps of Engineers V/cm volts per centimeter

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Contents

Summary ...... iii Acknowledgments ...... v Abbreviations and Acronyms ...... vii 1.0 Introduction ...... 1.1 2.0 Study Sites ...... 2.1 3.0 Methods ...... 3.1 3.1 Fish Species Composition, Abundance, and Habitat Use ...... 3.1 3.1.1 Determination of Pacific Lamprey Presence/Absence ...... 3.3 3.2 Taxonomic Composition and Abundance of Zooplankton, Phytoplankton, and Periphyton ...... 3.7 3.2.1 Zooplankton ...... 3.7 3.2.2 Phytoplankton and Periphyton ...... 3.8 3.3 Macroinvertebrate Distribution and Abundance ...... 3.9 3.4 Water Quality Monitoring ...... 3.11 3.4.1 Continuous Hourly Temperature ...... 3.11 3.4.2 Dissolved Oxygen and pH ...... 3.12 3.5 Sediment Composition and Organic Content ...... 3.13 4.0 Results and Discussion ...... 4.1 4.1 Study Conditions: Reservoir Elevation, Temperature, Discharge, Total Dissolved Gas, and Dam Spilling Operations ...... 4.1 4.2 Fish Species Composition, Abundance, and Habitat Use ...... 4.8 4.2.1 Salmonid Distribution ...... 4.8 4.2.2 Non-Salmonid Fish Community ...... 4.12 4.2.3 Determination of Pacific Lamprey Presence/Absence ...... 4.14 4.3 Taxonomic Composition and Abundance of Zooplankton, Phytoplankton, and Periphyton ...... 4.15 4.3.1 Zooplankton ...... 4.15 4.3.2 Phytoplankton and Periphyton ...... 4.18 4.4 Macroinvertebrate Distribution and Abundance ...... 4.23 4.4.1 EPT Index ...... 4.25 4.4.2 Family Diversity Index ...... 4.27 4.4.3 DEPT Index ...... 4.29 4.5 Water Quality Monitoring ...... 4.34 4.5.1 Water Temperature ...... 4.34 4.5.2 Dissolved Oxygen ...... 4.38

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4.5.3 pH ...... 4.41 4.5.4 Specific Conductance ...... 4.42 4.6 Sediment Composition and Organic Content ...... 4.42 5.0 Management Implications ...... 5.1 6.0 References ...... 6.1 Appendix A – Study Site Locations ...... A.1 Appendix B – Study Conditions ...... B.1 Appendix C – Fish Species ...... C.1 Appendix D – Zooplankton, Phytoplankton, and Periphyton ...... D.1 Appendix E – Macroinvertebrates ...... E.1 Appendix F – Water Quality ...... F.1 Appendix G – Sediment Composition ...... G.1

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Figures

2.1 Twelve locations evaluated on the lower Snake River ...... 2.2 3.1 Beach seine nets were deployed parallel to the shoreline at each site to collect juvenile fish ...... 3.2 3.2 Shocking sled as positioned within the 1.8-m-diameter test tank ...... 3.4 3.3 Voltage gradient within the boundaries of the net-pen ...... 3.5 3.4 Lamprey shocking sled used to conduct searches for juvenile Pacific lamprey in deepwater rearing habitat on the lower Snake River ...... 3.6 3.5 A Wisconsin-style plankton net was towed to the surface from a depth of 6 m to collect zooplankton samples at each sampling location...... 3.7 3.6 A Kemmerer bottle was used to collect phytoplankton from three depths at each sampling location ...... 3.8 3.7 Macroinvertebrates were sampled using artificial substrate deployed within rock baskets at each study site ...... 3.10 3.8 A Ponar dredge was used to collect sediment samples at each study site ...... 3.13 4.1 Mean daily forebay elevation in Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs over the 2010–2011 study period, compared with the 2008–2009 and 2001–2010 mean daily reservoir elevations ...... 4.2 4.2 Mean daily elevation (in the tailrace of Lower Granite, Little Goose, Lower Monumental, and Ice Harbor dams over the 2010–2011 study period, compared with 2008–2009 ...... 4.3 4.3 Mean daily reservoir temperature in Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs over the 2010–2011 study period, compared with the 2008–2009 and 2001–2010 mean daily reservoir temperatures ...... 4.4 4.4 Mean daily reservoir discharge in Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs during 2010–2011, compared to the 2008–2009 and 2001–2010 mean daily reservoir discharges ...... 4.5 4.5 Mean daily percentage saturation of TDG at lower Snake River reservoirs during 2010–2011 and 2008–2009 ...... 4.6 4.6 Mean daily reservoir spill in Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs over the 2010–2011 study period, compared with the 2008–2009 and 2001–2010 mean daily spill ...... 4.7 4.7 Number of salmonids sampled by season using seining and electrofishing ...... 4.9 4.8 Number of Chinook salmon found in each pool by seining and electrofishing ...... 4.9 4.9 Chinook salmon categorized into different run types ...... 4.10 4.10 NPMR projection graph depicting the relationship between electrofishing CPUE of juvenile Chinook salmon, river kilometer, and percentage gravel in dredge samples ...... 4.11 4.11 NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon, river kilometer, and percentage gravel in dredge samples ...... 4.11 4.12 Seasonal distribution of predator-size fish for seining and electrofishing ...... 4.12 4.13 Total number of predator-size fish found in each pool for seining and electrofishing ...... 4.13 4.14 Seasonal distribution of juvenile-size predator fish species for seining and electrofishing ...... 4.14

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4.15 Mean zooplankton densities measured per site throughout the study period ...... 4.16 4.16 Mean zooplankton densities measured per season in Lower Granite Reservoir locations ...... 4.17 4.17 Overall mean Chinook salmon sampled via electrofishing and overall mean zooplankton densities per transect ...... 4.17 4.18 Relative abundance of Daphnia found during September, the only month during which Daphnia were identified in notable quantities ...... 4.18 4.19 Relative abundance of Daphnia, percentage silt and fines, and percentage organic carbon measured per transect throughout the study period ...... 4.19 4.20 Mean phytoplankton and zooplankton densities measured per site throughout the study period ...... 4.19 4.21 Mean phytoplankton densities measured seasonally in Lower Granite Reservoir locations ...... 4.20 4.22 Mean phytoplankton biomasses and chlorophyll a content measured per site throughout the study period ...... 4.21 4.23 Mean phytoplankton biomasses measured per site per season in Little Goose and Lower Monumental reservoirs ...... 4.21 4.24 Mean phytoplankton chlorophyll a content measured per site per season in Little Goose and Lower Monumental reservoirs ...... 4.22 4.25 Mean periphyton biomasses and chlorophyll a content measured per site throughout the study period ...... 4.22 4.26 Mean periphyton biomasses measured per site per season in Ice Harbor Reservoir ...... 4.23 4.27 Mean periphyton chlorophyll a measured per site per season in Ice Harbor Reservoir ...... 4.23 4.28 Overall mean ETP relative abundance per transect, including other studies of first and second-order streams ...... 4.26 4.29 Mean macroinvertebrate diversity, by site ...... 4.27 4.30 Mean seasonal diversity, by site, in Lower Granite, Little Goose, Lower Monumental, and Ice Harbor Reservoirs ...... 4.28 4.31 Overall mean macroinvertebrate diversity, by site, on alluvium versus colluvium ...... 4.29 4.32 Mean DEPT biomass, by transect, with Chinook salmon sampled via electrofishing and seining ...... 4.30 4.33 NPMR projection graph depicting the relationship between seining CPUE of subyearling Chinook salmon, river kilometer, and biomass of DEPT macroinvertebrates ...... 4.30 4.34 Mean seasonal DEPT biomass, by site, in all reservoirs ...... 4.31 4.35 Overall mean DEPT biomass, by site, for alluvium substrate and angular colluvium substrate ...... 4.32 4.36 Mean spring macroinvertebrate DEPT biomass, by site, on alluvium versus colluvium ...... 4.32 4.37 Mean DEPT relative abundance, by site, with Chinook salmon sampled via electrofishing and seining ...... 4.33 4.38 Mean DEPT relative abundance in free-flowing and embayment areas of Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs ...... 4.34 4.39 Hourly temperature separated by season ...... 4.35 4.40 Diel fluctuations at Clarkston Lower for a 2-week time period from August 1, 2011, to August 15, 2011 ...... 4.36

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4.41 Temperature data from the deep, mid, and shallow sensors at Offield Landing Lower from November 2011 to October 2011, and during the time period August 15, 2011 to September 22, 2011, showing the temperature variation between deep and shallow sensors ...... 4.37 4.42 Boxplot showing the temperature difference between the deep and shallow sensors for each site ...... 4.38 4.43 Seasonal variability of dissolved oxygen with all sites combined ...... 4.39 4.44 Dissolved oxygen long-term Minisonde data showing elevated levels at Sheffler Shoal Lower ...... 4.40 4.45 Cluster analysis results showing site groupings based on trends in water quality ...... 4.40 4.46 Seasonal variability of pH with all sites combined ...... 4.41 4.47 Seasonal variability of specific conductance with all sites combined ...... 4.42 4.48 Percentage of sample for all sites combined across the lower Snake River for four size classes: gravel, medium to very coarse sand, fine to very fine sand, and silt and finer ...... 4.43 4.49 Gravel and fine to very fine sand for the various site types ...... 4.44 4.50 Notched box plots showing the percentage organic carbon across types of sites, pools, and sites where Chinook salmon were present or absent ...... 4.45 4.51 Notched box plots of the medium to very coarse sand fraction and silt and finer fraction for locations where Chinook salmon were present and absent ...... 4.46 4.52 NPMR projection graph depicting the relationship between electrofishing CPUE of juvenile Chinook salmon, river kilometer, and percentage gravel in dredge samples ...... 4.47 4.53 NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon, river kilometer, and percentage of fine to very fine sand in dredge samples ...... 4.47 4.54 NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon, river kilometer, and percentage of medium to very coarse sand in dredge samples ...... 4.48 4.55 NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon, river kilometer, and percentage of silt and finer sediments in dredge samples ...... 4.48 4.56 The number of juvenile Chinook salmon found over each predominant sediment type when normalized by the number of seine hauls conducted at each type of site ...... 4.49

Tables

3.1 Locations and dates where sediment samples were collected ...... 3.14 4.1 Dates and sizes of catch used to identify Chinook salmon runs ...... 4.10 4.2 Macroinvertebrate taxa collected from 24 sample sites throughout Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs during the November 2010–September 2011 sampling period ...... 4.24

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1.0 Introduction

The construction of Ice Harbor Dam (1955–1961), Lower Monumental Dam (1961–1976), Little Goose Dam (1963–1970), and Lower Granite Dam (1965–1975) has altered the downstream transport of sediments on the lower Snake River for nearly half a century (USACE 1996, 2010; CBR 2008). As sediment deposition continues, storage capacity, flow regulation, flood control, recreation, navigation, and many of the other benefits of hydropower diminish (Morris et al. 1998). In order to maintain the navigation channel and simultaneously mitigate for lost salmonid rearing habitat, the U.S. Army Corps of Engineers (USACE) is actively conducting research to determine whether in-water disposal of dredged sediments can be used to create additional shallow-water salmonid rearing habitat.

Fine sediments are often considered ecosystem contaminants by biologists and are not typically associated with aquatic integrity and productivity (Waters 1995; Seybold and Bennett 2010). However, out-migrating juvenile Chinook salmon (Oncorhynchus tshawystscha) have been observed to prefer gradual, lateral bed slope areas characterized by fine sediments in the lower Snake River (Curet 1993; Tiffan et al. 2006). In an effort to determine the benefits of this disposal method, habitat characteristics and biotic communities were monitored at test disposal sites and reference sites in Lower Granite and Little Goose reservoirs between 1988 and 2004 (Bennett et al. 1988b, 1991, 1993a, 1993b, 1995a, 1995b; Chipps et al. 1997; Seybold et al. 2007). Results of these studies showed that the species diversity and juvenile salmonid usage were enhanced at in-water disposal sites and that trophic structure among communities did not differ between reference and disposal sites. The USACE used many of these findings to assist with a July 2002 Dredged Material Management Plan/Environmental Impact Statement (DMMP/EIS) that defined the approach the USACE planned to follow for the next 20 years for managing sediment deposition. Subsequently, in November 2002, a lawsuit was filed challenging the environmental compliance of the DMMP/EIS.

In response to the continued need to remove accumulated sediment from the authorized navigation channel, the USACE is developing a Programmatic Sediment Management Plan/Supplemental Environmental Impact Statement for all four reservoirs on the lower Snake River. As part of this plan, research activities were recently expanded to evaluate water quality, biological integrity, and seasonal variability of habitat quality at locations within all four lower Snake River reservoirs (Seybold and Bennett 2010).

At the request of the USACE, Battelle–Pacific Northwest Division (Battelle) conducted a study to describe the fish community structure, habitat quality, and biological integrity of a select group of habitat complexes in the lower Snake River from fall 2010 through summer 2011. Study locations represent areas where sediment may be removed, sites where additional shallow-water rearing habitat has previously been or could potentially be created in the future, or locations that represent reference sites where high-quality rearing habitat for juvenile Chinook salmon is thought to currently exist. Through analysis of this information, the USACE hopes to gain a better understanding of existing high-quality shallow-water rearing habitat so that like habitat can be created using in-water disposal of upriver sediments following removal and relocation.

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Specifically, the objectives of our study were to • Monitor predator and juvenile salmonid species composition, abundance, and habitat use. • Monitor all life stages of bull trout (Salvelinus confluentus) and Pacific lamprey (Lampetra tridentata) presence and absence. • Assess taxa composition and abundance/density of zooplankton, phytoplankton, and periphyton. • Evaluate biological integrity based on the biomass and diversity of benthic macroinvertebrates. • Characterize water quality and sediment composition (including organic content).

To place results of these objectives in context with previous research conducted on all four reservoirs within the lower Snake River during 2008–2009, operational conditions (discharge, reservoir elevation, tailrace elevation, temperature, spilled discharge, and percentage saturation of total dissolved gas) were assessed during 2008–2009 and during 2010–2011. In addition, nonparametric multiplicative regression was used to relate metrics of habitat quality and evaluate the relative habitat quality at study locations.

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2.0 Study Sites

Twelve locations from throughout the four lower Snake River reservoirs were selected for our evaluation with input from staff biologists at the USACE, Walla Walla District (Seybold and Bennett 2010; Figure 2.1). Each site was subdivided further into upstream and downstream locations, yielding 24 sample sites. Sampling locations included areas where sediment could be removed in the future (i.e., Clarkston) and where in-water disposal of dredged sediment had been used to create shallow-water habitat in the past (i.e., Knoxway Bench Lower). However, the majority of the sampling locations represent areas the USACE considers existing high-quality shallow-water habitat. High quality shallow- water habitat was previously characterized as areas with low riverbed gradient, low velocity, and sandy substrates (USACE 2002). This determination was made based on research that showed subyearling Chinook salmon were consistently captured within areas that shared these characteristics on the Snake River (Bennett and Shrier 1986; Bennett et al. 1988a, 1990, 1991, 1993a, 1993b).

At each location, transects were oriented parallel to the shore in areas represented by a range of lateral slope gradients (in a direction perpendicular to the shore). Water depths were less than 6 m at all study sites. Sites within Lower Granite Reservoir were on the south shore of the impoundment and included Asotin Slough (river kilometer [rkm] 235.7–237.3), Clarkston (rkm 222.0–223.7), Knoxway Bench (rkm 187.4–189.1), Knoxway Bay (rkm 186.3–186.6), and Offield Landing (rkm 174.6–177.5). Asotin Slough Upper and Lower were least similar to other sample sites due to proximity to the Hells Canyon Reach. Asotin sampling locations were characterized by relatively swift currents and coarse riverbed substrates compared to all other study sites.

Clarkston Upper and Lower are adjacent to urban areas and include docks and pile structures, outputs for municipal waste water and runoff, and a developed shoreline. These sites have a gradual bed slope and are prone to silt deposition, with few coarse substrates near shore. Because of sedimentation and heavy industrial use of these areas, dredging has occurred here in the past. Downstream, Knoxway Bench Upper has a rapid bed slope of cobbles and talus and little shallow-water habitat. In contrast, the Knoxway Bench Lower site was previously modified using dredge disposal sediments to construct shallow-water habitat and is therefore characterized by a more gradual bed slope and composed of sand and silt. Knoxway Bench Lower was the only site previously modified to create shallow habitat using in- water disposal of dredged materials that was part of our study. The Knoxway Bay sites are on the east (Upper) and west (Lower) sides of an embayment, distal to a small tributary. Knoxway Bay Upper has a steep bed slope and consists of a mixture of sand and silt, while the bed slope of Knoxway Bay Lower is more gradual, with small amounts of coarser substrates embedded in sand and silt. There is an inundated grove of trees in the center of the embayment. Offield Landing Upper and Lower are 1.6 km upstream of Lower Granite Dam and are characterized by a steep bed slope with a substrate consisting of cobbles, interspersed with small patches of sand and silt near shore. The Knoxway Bench, Knoxway Bay, and Offield Landing sites are bordered by steep basalt cliffs at the water’s edge.

Illia Dunes (rkm 163.3–165.1) and New York Island (rkm 125.8–127.1) were located within the Little Goose impoundment. Illia Dunes Upper is 9.7–11.4 km downstream of Lower Granite Dam and has a gradual bed slope consisting of sand with few cobbles. Illia Dunes Lower was located within a predominantly shallow backwater area (< 2 m up to 100 m offshore), with a gradual bed slope of silt and some sand. Both Illia Dunes sites are on the southern shore. New York Island, situated mid-channel 12.7 km upstream of Little Goose Dam, was separated into a transect along its right bank on the north

2.1 Final Report side of the channel (termed “upper”) and a transect along the left bank on the south side of the island (termed “lower”). With the exception of a small cove on the north side of the island, New York Island Upper has a steep bed slope extending into very deep water. New York Island Lower has a gradual bed slope and consists of sand and few cobbles, with large expanses of shallow, silty nearshore habitat (< 2 m up to 50 m offshore).

Figure 2.1. Twelve locations evaluated on the lower Snake River (rkm = river kilometer; Snake River mouth = 0). Each site was divided further into an upper reach and a lower reach. Site types were grouped further based on differences in bed slope and flow characteristics (blue circles = free flowing; red circles = shallow bed slope; green circles = steep bed slope; yellow circles = backwater areas).

Tucannon River (rkm 99.8–100.6) and Devil’s Bench (rkm 69.2–70.8) are located within the Lower Monumental impoundment, on its south and north shores, respectively. Tucannon River Upper is located at the eastern edge of the mouth of the Tucannon River, within a coved area bordered by steep basalt cliffs at the water’s edge. This shoreline is armored with cobbles and talus but quickly gives way to dominant sand on a gradual slope. The majority of the site is less than 4 m deep and is often frequented by fishermen. Tucannon Lower is downstream of the Tucannon’s delta, in the main-stem channel. The lower site is characterized by a steep rip rap embankment, extending from the roadbed to a rapidly sloping riverbed. Substrate in the vicinity is dominated by large talus that transitions into sand nearer the delta. Devil’s Bench is located 2.3 km upstream of Lower Monumental Dam and is bordered by steep basalt cliffs. Devil’s Bench Upper is located in a cove with a gradual bed slope and consists of sand, silt, and few cobbles. Devil’s Bench Lower is in the main-stem channel, with a rapidly sloping bed of sand and cobble.

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Burr Canyon (rkm 58.9–60.5), Burr Shoal (rkm 51.6–53.9), and Sheffler Shoal (rkm 43.4–45.1) are contained within the Ice Harbor impoundment. Burr Canyon Upper is located 8 km downstream of Lower Monumental Dam in a sheltered site with a gradual bed slope and consists of cobble and some sand. Burr Canyon Lower also has a gradually sloping, primarily cobble bed. Burr Canyon is adjacent to a roadbed on the north shore of the river. Burr Shoal Upper is predominantly sandy and shallow (< 2 m up to 80 m offshore); the bed does not exceed this depth within much of the sample site. The shoreline is characterized by mixed agricultural use (e.g., fruit orchards, alfalfa hay farms, and vineyards). Burr Shoal Lower has a gradual slope of sand and cobble. Both Sheffler Shoal Upper and Lower have gradual slopes with bottoms consisting of sand and cobble. Both the Burr Shoal and Sheffler Shoal sites extend along the south shore of the river.

Maps showing the size, area, and detailed locations where various types of samples were collected are included in Appendix A.

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3.0 Methods

3.1 Fish Species Composition, Abundance, and Habitat Use

Principal methods used to sample the fish community included boat electrofishing, beach seining, and snorkeling. In addition, electroshocker surveys were conducted to determine the presence/absence of juvenile Pacific lamprey.

Boat electrofishing was conducted using an electrofishing boat (Model EH, Smith-Root, Inc., Vancouver, Washington) outfitted with a generator-powered pulsar (GPP) electrofisher (120 pulses/s, 3–5 amps, 250–350 V; Smith_Root). Sampling was initiated in January 2011 and conducted every 3 weeks from April through June 2011. Summer (late July and August) electrofishing was not conducted due to high water temperatures (>64°F) as required by our federal National Oceanographic and Atmospheric Administration permit. On each trip, electrofishing began at least 1 d prior to other fish/habitat sampling efforts. Electrofishing was conducted primarily during nocturnal hours at predetermined locations on each sampling transect (Appendix A). Generally, electrofishing transects were nearly as long as each study site, and each subsequent trip sampled the same area. The starting and ending points of each electrofishing drift were recorded and provided to snorkelers so they could sample the same locations. Each electrofishing effort consisted of one 10-min shocking interval at each station that equated to an approximately 600-m-long reach within each transect. All fish were netted, identified to species (Scholz and McLellan 2009), measured for total length, weighed, and released. Adult salmon and all life stages of bull trout and lamprey were noted in a field book and released immediately during all sampling.

We also used a beach seine (i.e., a 30-m × 2.5-m seine with 14.5-m3 bag; 6.4-mm mesh) to catch juvenile salmonids and other resident fish species. The seine was set parallel to and approximately 15 m from shore with attachment lines, then pulled perpendicular to shore to sample an area of approximately 460 m2 on each haul (Figure 3.1). One seine haul was made at the same location for each transect on the specified sampling date when conditions allowed (Appendix A).

Juvenile salmon and resident fish were enumerated and measured for length and weight. Juvenile salmon were sedated in an aerated bucket of river water with a dose of 40 mg tricaine methanesulfonate

(MS-222)/L of water and an equal amount of sodium bicarbonate (NaHCO3) prior to being measured and weighed. Once lengths and weights were obtained, fish were allowed to recover from anesthesia in large aerated containers of fresh water for at least 10 min after they regained equilibrium. All fish were returned to the river near the location they were caught. Any fish unable to regain equilibrium after 10 min were euthanized with a dose of 250 mg/L MS-222 and recorded as an incidental mortality. A subsample of fish was measured if catch rates were high. If more than 50 fish of a given species were present, at least 20 fish were selected randomly and measured.

Snorkeling was used to identify fish species present at each site following electrofishing and seining efforts (Wydoski and Whitney 1979). Snorkeling was effective during fall (September), winter (January), and late summer (August) periods; however, visibility prevented the use of snorkeling during spring and early summer (April–early July) sampling. Snorkelers floated in a downstream direction parallel to the shoreline in shallow water (<1.5 m deep) in areas that corresponded to electrofishing transects. Fish species, number, and substrate type were recorded on an underwater data cuff.

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Figure 3.1. Beach seine nets were deployed parallel to the shoreline at each site to collect juvenile fish.

Statistical differences were considered for salmonids and predators seasonally and annually with results grouped by project, type of site, location (i.e., which of the 12 general study sites), and transect (i.e., which of the 24 individual transects). Sites were further grouped into four different categories: free- flowing river (Asotin Slough Upper and Lower), backwater/tributary delta (Knoxway Bay Upper and Lower, Illia Dunes Lower, Tucannon River Upper, Devil’s Bench Upper, and Burr Shoal Upper), gradual bed slope main-stem reaches (Clarkston Upper and Lower, Knoxway Bench Lower, Illia Dunes Upper, New York Island Upper and Lower, Burr Canyon Upper and Lower, Burr Shoal Lower, Sheffler Shoal Upper and Lower), and steep bed slope main-stem reaches (Knoxway Bench Upper, Offield Landing Upper and Lower, Tucannon River Lower, Devil’s Bench Lower). Data were compiled using Microsoft Excel. Electrofishing and seining data were evaluated using Kruskal–Wallis tests followed by Mann– Whitney U-tests if significant differences were found (both using SigmaPlot Version 11.0; Systat Software Inc., San Jose, California). During water-level fluctuations that occurred in spring 2011, some seining locations could not be sampled on all trips. Thus, seining data were not as uniformly represented as electrofishing data, and statistical comparisons using seining data were limited.

Cluster analyses were performed in an effort to group locations relative to water quality and habitat suitability. Similarities and differences in water quality (dissolved oxygen [DO], conductivity, pH) and substrate composition (gravel, fine to very fine sand, medium to very coarse sand, silt and finer) were evaluated using program JMP (Version 8.0; SAS Institute). Transects with values close to each other relative to other transects were grouped into clusters; the distance between two clusters was computed as the average distance between pairs of observations.

Nonparametric multiplicative regression (NPMR; McCune 2006) was used to identify relationships between subyearling fall Chinook salmon seining catch-per-unit-effort (CPUE) and a host of predictor variables (river kilometer; DO; conductivity; pH, percentages of gravel, medium to very coarse sand, fine to very fine sand, silt and finer; percentage of organic content; mean zooplankton density; Daphnia abundance; mean macroinvertebrate diversity; mean Diptera + Ephemeroptera + Plecoptera + Trichoptera [DEPT] macroinvertebrate biomass; mean DEPT macroinvertebrate abundance, and predator

3.2 Final Report electrofishing CPUE). This approach was also used to identify relationships between Chinook salmon electrofishing CPUE and the above-mentioned predictor variables. Program HyperNiche (McCune and Mefford 2009) was used to perform NPMR analyses, whereby variables were added in a forward stepwise fashion and leave-one-out cross-validated statistics were used to reduce overfitting (McCune 2006). Model fit (xR2) was evaluated by the size of the residual sum of squares in relationship to the total sum of squares (McCune 2006). The model with the highest xR2 value that did not violate overfitting criteria was selected as the “best” model. Additional models were also evaluated, as presented in Section 3, Results.

3.1.1 Determination of Pacific Lamprey Presence/Absence

In response to the need for a cost-effective, minimally obtrusive sampling technique to determine the presence/absence of juvenile Pacific lamprey, we developed a new tool designed to work in deepwater habitats in excess of 8 m that does not require handling sampled individuals. Prior to field deployment, we tested the effective sampling area and shocking efficiency of our new technique at Battelle’s Aquatic Research Laboratory in Richland, Washington. Development of our new technique was completed during spring 2011 when turbidity on the lower Snake River was relatively high (>4 NTU) and searches for juvenile lamprey were not feasible. When turbidity decreased below 4 NTU (during late July), field searches were conducted at 24 study sites on the lower Snake River; the surveys were conducted during late July and September 2011.

3.1.1.1 Laboratory Test to Evaluate New Sampling Method

Electrofishing technologies used to sample for lamprey ammocoetes in deepwater environments in the Pacific Northwest and the Great Lakes were reviewed in Mueller et al. (in press). Mueller et al. also provide a thorough description of a laboratory assessment to determine the efficacy of the new electrofishing technique. In general, the method was evaluated in the laboratory using western brook lamprey (Lampetra richardsoni) ammocoetes. A total of 30 western brook lamprey, ranging in total length from 70 to 150 mm (mean = 115 mm), were acquired via backpack electrofishing from the Little Klickitat River (near Goldendale, Washington) in late March 2011. Lamprey were transported to Pacific Northwest National Laboratory in Richland, Washington, where they were held in two 37.8-L aquaria supplied with a mixture of groundwater and Columbia River water. Fish were acclimated from a temperature of 7°C to 10°C over a 3-d period and held in the aquarium for 6 d to allow fish to acclimate to the substrate type and water supply. Prior to testing, lamprey were placed in a rectangular test pen (66.0 cm × 83.8 cm × 83.8 cm high) constructed from 4-mm plastic mesh screen fastened to a plywood base. The pen was supported by a frame constructed of 19-mm-diameter polyvinyl chloride pipes. The pen was placed in a round fiberglass tank (1.8 m in diameter × 1.2 m high), slightly elevated above the bottom of the tank to allow water to flow under the plywood base and down the drain. Sediment consisting of coarse sand and finer particles was placed in the pen to a depth of 8.9 cm. By mass, 83% of the sediment consisted of particles that had a diameter finer than 1.0 mm. Of that 83%, 50% consisted of particles between 0.25 mm and 0.5 mm in diameter. The tank was then filled with water to a depth of 0.86 m.

A weighted sled was used to shock juvenile lampreys and film their response (Mueller et al. in press; Figure 3.2).

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Three trials were conducted using 10 lampreys per trial. Lampreys were released into the test tank and allowed to swim to the bottom of the pen and burrow into the substrate, a process that generally took less than 5 min. Video recordings were made to determine the approximate location where each ammocoete burrowed. Shocking began approximately 3 h after all lampreys had burrowed into the substrate. Following the tests, recorded tapes were reviewed to verify the approximate lamprey location as they burrowed into the substrate and to count the number of lampreys that emerged. Detection efficiency, defined as the percentage of lampreys released into the tank that were observed emerging from the substrate, was calculated for each trial and by pooling results from the three trials. The amount of time taken by each lamprey to emerge from the substrate was also noted. After each test, all lampreys were collected, anesthetized with MS-222 (250 mg/L), measured to the nearest millimeter, and transferred to a separate aquarium where they were held for 48 h and monitored for post-shocking and handling mortality.

Figure 3.2. Shocking sled as positioned within the 1.8-m-diameter test tank.

Voltages during shocking ranged from 0 V/cm at the edge of the measured region to 0.92 V/cm near one of the electrodes. The average voltage for the entire region within the base of the net-pen was 0.34 V/cm with slightly higher readings near the electrode locations (Figure 3.3).

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Figure 3.3. Voltage gradient (V/cm) within the boundaries of the net-pen. The rectangular region encompassed by the four electrodes (dashed line) and electrode location is illustrated. Electrodes on the left were cathodes; electrodes on the right were anodes.

3.1.1.2 Field Searches for Pacific Lamprey

Two surveys were conducted to search for Pacific lampreys at each of the 24 lower Snake River study sites; one occurred during the week of July 25, 2011, and the other occurred during the week of September 25, 2011. Sampling points were evenly distributed from randomly selected locations within each individual transect. Sampling points were distributed throughout the entire area of each transect in an effort to determine whether juvenile lamprey were present or absent there. The bounds of each transect used for juvenile lamprey searches were identical to the bounds used for other fish sampling and habitat quality studies conducted as part of this project. Locations where searches for juvenile lamprey were conducted were mapped using a geographic information system. During searches, boat navigation relied upon an on-board, real-time differential Global Positioning System (DGPS) receiver (Trimble GPS Pathfinder Pro XR, Sunnyvale, California) that also collected positional data during the surveys. The integrated DGPS beacon receiver and antenna provided DGPS corrections to calculate accuracy to less than approximately 0.5 m. The DGPS and video system were synchronized via a time stamp. Within each sampling location, transects were established perpendicular to flow using approximately 70-m spacing. Within transects, shocking was conducted at approximately 30-m intervals. For each survey, videotapes were reviewed to determine an average video coverage (sampling area) for each polygon.

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Video coverage area was calculated using ArcGIS Version 9.3 software (Environmental Systems Research Institute, Inc., Redlands, California).

During surveys, a boat-deployed video system consisting of a high-sensitivity remote camera (Model SDC-MAL, Sartek Industries, Inc., Medford, New York) was attached to a weighted platform (Groves and Garcia 1998) deployed from the research vessel. An integrated video/tow cable attached to a manual winch with slip ring mechanism was used to raise and lower the platform to the desired depth. Recordings were made using an 8-mm digital recorder (Sony Model GVD 7000); two high-resolution monitors for real-time viewing of the video were used in conjunction with the recorder. Recorded tapes were reviewed to verify observations made in the field. Turbidity was recorded using a Hach turbidimeter (Model 2100). The shocking system included underwater red lasers (Model HL6312G, C-Map Systems, Inc., Red Lodge, Montana) to provide a reference scale within the camera image so that substrate sizes could be determined at locations where lamprey were identified. The shocking sled used four electrodes (two on each side of the sled) deployed in a rectangular pattern, 25 cm apart on one side and 48 cm apart on the other side, and secured to the outer portions of the lead weights (Figure 3.4). Electrodes extended to a length of about 50 cm depth, with the lower 5 cm contacting the substrate. A modified, ABP-2 backpack electroshocker unit (ETS Electrofishing, LLC, Verona, Wisconsin) powered by a 12-V deep-cycle high amp-hour battery with 16/2-gauge conductors was used to deliver the current. The total cable length from the portable control unit to the sled was 8 m. During each trial, the shocking system delivered a 100- to 200-V, 4-Hz, 25% duty cycle and a 3:1 burst rate pulse for 30–45 s at each sampling location.

Figure 3.4. Lamprey shocking sled used to conduct searches for juvenile Pacific lamprey in deepwater rearing habitat on the lower Snake River.

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3.2 Taxonomic Composition and Abundance of Zooplankton, Phytoplankton, and Periphyton

3.2.1 Zooplankton

A Wisconsin-style plankton net (80-μm mesh, 12.7-cm mouth opening) was used to sample zooplankton from a representative location (consistent depth, current) at each of the 24 study transects on seven sampling events that coincided with fish sampling (Figure 3.5). The net was lowered from the boat to an approximate depth of 6 m; once vertical, it was slowly (0.5 m/s) towed to the surface. Each tow sampled roughly 75 L of water. The planktonic material was then decanted into a container (250-mL Nalgene bottle) using deionized water and diluted to 225 mL with a mixture of deionized water and 15 drops (0.75 mL) of preservative Lugols solution (20 g KI + 10 g I/L).

Figure 3.5. A Wisconsin-style plankton net was towed to the surface from a depth of 6 m to collect zooplankton samples at each sampling location.

In January, one vertical tow was conducted at each site. Because low numbers of zooplankton were subsequently observed, sampling efforts quadrupled from April through September, with four vertical tows being conducted per site. Each of the vertical tows was decanted into the same sample jar per site, and the amount of preservative Lugols solution added was increased to 45 drops (2.25 mL).

Zooplankton samples were stored in a refrigerated, dark location for up to 2 months prior to analysis. In the laboratory, samples were enumerated and identified to the lowest practical level of taxonomy. Numerical abundance (by lowest practical taxon), relative abundance (by lowest practical taxon), and density (overall) were calculated by site and by season. The relative abundance of Daphnia was highlighted due to its importance to juvenile salmonid diets (Haskell et al. 2006). The density of zooplankton, or number of individuals represented by each taxa per liter of water, was extrapolated from the volume of water (75 or 300 L of water, depending on month) sampled at each transect, assuming 100% efficiency. These densities were compared, statistically, across all sites, between unmodified and modified sites, sites where Chinook were found and sites where they were absent, seasons, reservoirs, and

3.7 Final Report site characteristics (free-flowing reaches, embayment areas, main-stem areas with a gradual lateral bed slope, and main-stem areas with a steep lateral bed slope) using a Kruskal–Wallis one-way analysis of variance. Where significant differences were found, a Dunn’s pairwise multiple comparison test was completed to ascertain specific site-to-site significant differences.

3.2.2 Phytoplankton and Periphyton

Phytoplankton was sampled from a representative location (consistent depth, current) within each of the 24 transects. A Kemmerer bottle was lowered from the stationary boat to three different depths (1 m from the bottom, mid-depth, and 1 m from the surface) to collect phytoplankton samples (Figure 3.6). Approximately 0.33 L from each of the three depths was combined to provide a composite, depth– integrated sample of 1.0 L. Lugols solution (45 drops or 2.25 mL) was used as a preservative.

Figure 3.6. A Kemmerer bottle was used to collect phytoplankton from three depths at each sampling location.

Phytoplankton samples were placed on ice and stored in a dark location prior to analysis. In the laboratory, samples were enumerated and identified to the lowest practical level of taxonomy, most often genus, with differentiation made between diatomaceous, hard taxa, and soft taxa. Density, or number of individuals per liter, was extrapolated from the numerical abundance in each subsample identified by EcoAnalysts, assuming 100% efficiency. For each site, ash-free dry mass (AFDM) analysis was executed for each whole sample after taxonomy was completed. Chlorophyll a values were then determined for each sample from this AFDM of the sample using published values, or 1.5% of the measured AFDM (Eaton et al. 1995).

Periphyton was sampled from artificial substrates deployed alongside rock baskets at each of the 24 transects. These artificial substrates consisted of four construction bricks (763 cm2) deployed on a

3.8 Final Report long-line, in which bricks were spaced approximately 0.5 to 1.0 m apart. Brick lines were deployed on the first sampling event and recovered and redeployed every 3 months thereafter. This sampling interval was based on research conducted by Lamberti and Resh (1985), who showed that a 63-d exposure period for introduced substrates accurately represented natural periphytic density and species composition. Periphyton was sampled using a 5-cm2 sampling frame placed across the face of the brick exposed to the photic zone. All periphytic material within this frame was scraped from the surface, decanted with deionized water, and preserved with Lugols solution before being stored in a 250-mL Nalgene container. A Secchi disk was used to ensure that all periphyton was sampled from within the photic zone, and USACE data on reservoir elevation and river discharge were used to help determine appropriate sampling depths. Periphyton samples were preserved and stored in a cool, dark location for up to 2 months. From each sample, individuals were enumerated and identified to genus. AFDM analysis was executed for each whole sample after taxonomy was completed. Chlorophyll a values were then determined for each sample from this AFDM of the sample using published values (Eaton et al. 1995). The same statistical tests conducted for zooplankton and described above were also conducted for phytoplankton and periphyton.

3.3 Macroinvertebrate Distribution and Abundance

Three different methods were used to characterize macroinvertebrate communities: Ponar dredge, kick net, and artificial substrate. At each of the 24 study transects, benthic macroinvertebrates were sampled from soft substrates (pebbles, sands, and fine sediments with a diameter less than 4 mm) using a Ponar dredge in deepwater areas concurrent with sediment sampling (April, July, and January). A kick net was used in shallow-water areas during seven sampling events. Rock baskets were deployed over hard substrates at all 24 sites to allow for comparison of taxa present across study locations.

Method selection for Ponar dredge and kick-net sampling was guided by composition of the riverbed. For example, Wise and Molles (1979) showed that the taxa Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Diptera preferred gravel that was between 10 and 25 mm in diameter. Flecker and Allan (1984) found that loose gravel and cobble—with ample interstices—provided a more productive habitat than embedded substrates for aquatic insects.

Artificial substrates consisted of wire baskets filled with 20 to 30 basalt colluvium and granitic alluvium in equal portions (Figure 3.7). Each rock type was purchased at local nurseries, sorted into size classes of 28 to 46 mm and 47 to 60 mm in diameter, and distributed evenly into wire baskets (Wildco, Buffalo, New York) measuring 25.4 cm long × 16.5 cm in diameter (Mason et al. 1967; Stark 2001).

Our approach was guided by previous studies utilizing artificial substrates in smaller-order streams than the Snake River (Cummins and Lauf 1969; Williams and Mundie 1978; Wise and Molles 1979; Khalaf and Tachet 1980), which showed that benthic invertebrate colonists exhibit a preference for particle size (Voshell 2002), and that while total biomass is greatest on “medium” gravel (mean diameter of ~ 24.2 mm), species diversity peaks on larger gravel (mean diameter of ~ 40.8 mm). A recent study on the Hanford Reach of the Columbia River included such baskets filled with 10 to 15 rocks measuring 40 to 60 mm in diameter (Stark 2001). Rock type was also chosen on the basis of surface heterogeneity: we hypothesized that rock with proportionally higher surface heterogeneity (basalt colluvium) could be expected to harbor more individuals than rock with proportionally lower surface heterogeneity (granitic alluvium).

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Figure 3.7. Macroinvertebrates were sampled using artificial substrate deployed within rock baskets at each study site.

At each site, two rock baskets were deployed over similar-size substrates that were located during the first sampling event using an underwater video camera and available bathymetric data. One basket was sampled for macroinvertebrates and redeployed on each of the seven subsequent trips, while the other was sampled concurrent with dredge sampling (April, July, and January). The extent of the photic zone at each site was determined with a Secchi disk, and rock baskets were lowered within this zone, or approximately 5 ft from the surface at each site (Mason et al. 1967). Proximity to the subsurface photic zone is paramount to secondary productivity (Mason et al. 1967; Kaster and Jacobi 1978), and macroinvertebrate diversity is typically negatively related to depth (Brooks et al. 2005). Therefore, rock basket locations were shifted slightly following each sampling event to accommodate seasonal changes in reservoir depth. During retrieval, baskets were carefully lifted to avoid contact with the river bottom, placed in a bucket, and cleared of attached macroinvertebrates.

All dredge samples were passed through a 0.595-mm sieve and then preserved—as were kick-net samples—in a 70% isopropyl alcohol solution. Samples were enumerated and identified to class for Oligochaeta and family for all other invertebrates in the laboratory (Merritt and Cummins 1996; Thorp and Covich 2010). All samples were analyzed as 1) a composite representation of a site’s benthos from shallow to deep water and 2) separately, by rock type, for biomass, numerical abundance (by family), relative abundance (by order), and diversity (by family). We also calculated the relative abundances of Ephemeroptera + Plecoptera + Trichoptera (EPT)—i.e., taxa known to be sensitive to habitat disturbances—and Diptera + Ephemeroptera + Plecoptera+ Trichoptera (DEPT)—taxa most important to juvenile salmonid diets in the Snake and Columbia rivers (Becker 1970, 1971; Edwards et al. 1974; Schreffler et al. 1992; Curet 1993; Merritt and Cummins 1996; Angradi 1999; Cover et al. 2008). All calculations were made on the basis of sample site and season.

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Diversity was expressed via Shannon’s Diversity Index

H' = -∑ pi ln pi where the relative abundance (pi) is ni/N; ni, is the abundance in a given taxon (in this case, family); and N is overall abundance. This metric incorporates measures of both taxonomic richness (the number of taxa) and evenness (the distribution of abundance among taxa in a community; Wilsey and Potvin 2000).

For each new taxa (family) found in our samples, a specimen was photographed next to a millimeter scale. Total biomass was determined using the length–mass equation

M = aLb where M is mass (milligrams), L is any linear dimension (millimeters), and a and b are constants that vary by order and family (Benke et al. 1999; Sabo et al. 2002; Meyer and Whiles 2008). Individuals sampled from classes Bivalvia and Gastropoda were included in all analyses except biomass. No published data were available for length conversion of the families Sphaeriidae, Lymnaeidae, Physidae, Planorbidae, Bithyniidae, or the class Polychaeta to dry mass. In contrast, constants for the length conversion of family Corbiculidae, have been published and were utilized (Benke et al. 1999; Sabo et al. 2002).

DEPT relative abundance, overall macroinvertebrate community diversity, and DEPT biomass found at each site on each sampling event were compared statistically using a Kruskal–Wallis one-way analysis of variance. Where significant differences were found, a Dunn’s pairwise multiple comparison test was completed to ascertain specific site-to-site significant differences. The same statistical tools were employed to compare unmodified and modified sites, sites where juvenile Chinook salmon were found and sites where they were absent, seasons, reservoirs, and site characteristics (free-flowing reaches, embayment areas, main-stem areas with a gradual lateral bed slope, and main-stem areas with a steep lateral bed slope). A literature review was also conducted to anticipate the responses of each new taxa (order and family) found on the lower Snake River to the sudden influx of fine sediments to benthic interstices.

3.4 Water Quality Monitoring

3.4.1 Continuous Hourly Temperature

At each of the 24 sampling locations, we established one temperature monitoring station where depth- discrete temperature data were collected hourly from November 2010 to October 2011 (Appendix A). At each location, temperature was measured at three vertical locations (1 m above the riverbed, mid water column, and ~1 m below the water surface). Temperature monitoring was conducted using water temperature data loggers (HOBO Model HOBO Pro v2, Onset Computer Corporation, Pocasset, Massachusetts), which have an accuracy of 0.2°C between −20°C and 70°C. Temperature loggers were attached to a galvanized wire rope (1/4 in. diameter) and anchored to the riverbed with a 100-lb steel block. The top end of the cable was floated with a mooring buoy. The shallow and middle sensors were attached to the main wire rope with a 10-lb weight attached directly below the middle sensor. The length of the wire rope was approximately double the depth at which they were deployed, to allow for changing water levels and easy retrieval with a davit arm and geared hand crank. The deep sensor was attached to a

3.11 Final Report separate line (1/2-in. floating poly rope) that was also attached to the 100-lb steel block. This line was 1.5 m long and had the sensor attached at 1 m above the bottom with a crab buoy at the end to keep it floating vertically. Loggers were downloaded, serviced, and redeployed on each of the seven sampling trips following the initial trip when they were deployed. Data were unavailable from Tucannon River Upper (all three sensors) from June 15, 2011, to September 22, 2011; Asotin Slough Lower (deep sensor) from February 5, 2011, to September 22, 2011; Clarkston Upper (deep sensor) from May 8, 2011, to September 22, 2011; and Offield Landing Upper (shallow sensor) from July 11, 2011, to September 22, 2011. These data gaps were caused by vandalism (Tucannon River), high flows (Asotin Slough), excessive sedimentation (Clarkston), or equipment failure (Offield Landing).

Statistical differences were considered seasonally with all sites combined and on an annual interval between pools, type of site, transect, where juvenile Chinook salmon were present, and where they were absent. We visually looked for statistical differences between mean values from different monitoring locations and groupings using notched boxplots. To reduce temporal autocorrelation associated with 12- and 24-h diel cycles, we used a randomly selected subset of each overall data set for the notched box plots. One data point per hour was randomly selected within every 12-h period to facilitate these tests. Data were compiled and analyzed using Microsoft Excel and R (R Development Core Team 2011). Significant differences were determined using notched box plots, which were created using R as outlined by Chambers et al. (1983) and Frigge et al. (1989). Notches within box plots represent the uncertainty about the medians. Overlapped notches indicate that the medians of the two groups significantly differ at the 95% confidence level. The center of the notched plot is the median, and the upper and lower bounds are the 25th and 75th percentiles. When the confidence intervals surpass the interquartile range, the notches do not fall within the boxes. This is due to large variability in the data and is compounded by small sample size. Circles indicate outliers.

3.4.2 Dissolved Oxygen and pH

Dissolved oxygen (DO), pH, specific conductance, temperature, and depth were measured on each of eight visits by deploying a data-logging water quality sonde on the riverbed and slowly raising it to the river surface while logging data every second (Appendix A). This allowed data collection at approximately 0.2-m intervals, allowing us to measure vertical gradients in water quality that were present. Water quality was measured using Hydrolab Minisonde 5 sensors (Hach Environmental, Loveland, Colorado). Parameters measured by the Hydrolab sensors (with stated accuracies in parentheses) included DO (0.2 mg/L), pH (0.2 unit), specific conductance (2 µS/cm), depth (5 cm), and temperature (0.18°C). For depth-discreet measurements, Hydrolab sensors were calibrated within 2 d of recording field measurements and DO and depth were calibrated every day in the field. Sensors were calibrated according to the manufacturer’s specifications (Hach Environmental 2011).

In addition, we conducted hourly monitoring of DO and specific conductance at several locations during April–June 2011. During this period, site visits were conducted every 3 weeks, which equated to the approximate battery life of water-quality sensors. Monitoring locations were chosen at Knoxway Bench Upper and Lower because the lower site had been previously modified. The other monitoring sites included Clarkston Lower, Sheffler Shoal Lower, and New York Island Lower (allowing for a range of upstream to downstream locations to be sampled). At each location, one Hydrolab sensor was attached to the wire rope to which the Onset temperature sensors were also attached. The sensor was downloaded and redeployed on each of the April–June sampling trips. Some sensors were removed from the field due

3.12 Final Report to probe malfunction. All five locations sensors were deployed during early April 2011. On the first deployment the DO sensor at New York Island Lower site failed, data was discarded, and the sensor was subsequently removed from the river. The sensor at Clarkston Lower was removed following the second deployment because it had become waterlogged. The sensor at Sheffler Shoal Lower was used for the first two deployments but recorded data for only one day on the second deployment. On the third deployment (May 24 through June 15), the sensor at Sheffler Shoal Lower failed, data were discarded, and the sensor was removed from the river. Sensors at Knoxway Bench Upper and Lower recorded data during the entire season (April–July 7) and did not experience any probe failures.

Statistical differences were looked at seasonally with all sites combined and on an annual interval between pools, type of site, transect, where Chinook salmon were present, and where Chinook salmon were absent. Data were compiled and analyzed in Microsoft Excel. Significant differences were also determined using notched box plots, which were created using R, an open-source statistical software and data analysis program, similar to SAS, SPSS, and Stata.

3.5 Sediment Composition and Organic Content

A Ponar dredge was used to collect substrate samples from 3 locations at each of the 24 study transects on three separate sampling events that occurred in January, early April, and July (Figure 3.8; Appendix A). Sample locations were evenly distributed throughout the study site beginning from a randomly selected initial location at a depth similar to where temperature monitoring occurred (typically between 4.5 and 6 m). Three attempts were made to collect a sample before the site was assumed to consist of gravel larger than 2 mm (Table 3.1).

Figure 3.8. A Ponar dredge was used to collect sediment samples at each study site.

Substrate samples were dried inside a vented oven at 105°C for 24 h. The dried samples were sieved into 1-phi size classes from 64 mm (−6 phi) to 0.062 mm (4 phi). For each sample, the weight of the substrate in each size class was determined, yielding a percentage-by-weight value for each size class. All laboratory sample handling and quality assurance/quality control followed the guidelines of Guy (1969).

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Table 3.1. Locations and dates where sediment samples were collected. Site Number of sediment samples collected Winter(a) Spring(a) Summer(a) Asotin Slough Upper 0 0 0 Asotin Slough Lower 3 3 3 Clarkston Upper 3 3 3 Clarkston Lower 3 2 3 Knoxway Bench Upper 3 3 3 Knoxway Bench Lower 3 3 3 Knoxway Bay Upper 3 2 3 Knoxway Bay Lower 2 3 3 Offield Landing Upper 2 3 3 Offield Landing Lower 3 2 3 Illia Dunes Upper 3 3 3 Illia Dunes Lower 3 3 3 New York Island Upper 3 3 2 New York Island Lower 3 3 3 Tucannon River Upper 3 3 3 Tucannon River Lower 3 2 2 Devil’s Bench Upper 3 3 3 Devil’s Bench Lower 3 3 2 Burr Canyon Upper 2 2 3 Burr Canyon Lower 3 3 3 Burr Shoal Upper 3 3 3 Burr Shoal Lower 3 2 3 Sheffler Shoal Upper 3 2 3 Sheffler Shoal Lower 3 3 3 (a) One sampling trip was conducted at each location during each season. The maximum number of samples that could have been collected from a given site was nine.

The organic carbon content of sediments less than 2 mm diameter in size (“fine”) was determined using the loss on ignition method (Heiri et al. 2001). When possible, a 20-g sample of the fine sediment was taken from each sample. If less fine sediment was available, the entirety was taken for the loss on ignition method. Samples were fired at 550°C for 4 h in a muffle furnace. The difference between their mass before the furnace and the mass afterward was calculated as the percentage organic carbon.

Size classes were lumped into four different categories. These included gravel (2 mm–>64 mm), medium to very coarse sand (0.25 mm–2 mm), fine to very fine sand (0.063 mm–0.25 mm), and silt and finer (<0.063 mm). Statistical differences were considered on an annual interval between pools, type of site, transect, where Chinook salmon were present, and where Chinook salmon were absent using notched box plots. Data were compiled and analyzed using Microsoft Excel and R.

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4.0 Results and Discussion

To provide context with previous research conducted on the lower Snake River, we compiled reservoir elevation, temperature, discharge, and spill data for the four lower Snake River projects during 2010–2011. The same data were summarized for 2008–2009, when similar research was completed on the lower Snake River (Seybold and Bennett 2010). Both periods were then compared to the 10-year, 2001–2010 average. Collectively, these data may be useful for comparison to our habitat quality results in assessing whether or not metrics of habitat quality are influenced by operational conditions during different water years. Comprehensive study condition data are included in Appendix B.

4.1 Study Conditions: Reservoir Elevation, Temperature, Discharge, Total Dissolved Gas, and Dam Spilling Operations

Mean daily reservoir elevations for the 2010–2011 study period in Lower Granite, Little Goose, Lower Monumental, and Ice Harbor Reservoirs were similar to elevation data from 2008–2009, although both were lower than 10-year averages for these reservoirs (Figure 4.1; UW 2011). This difference was significant in all reservoirs except Lower Monumental; here, 2010–2011 reservoir elevation was significantly lower than the 10-year average, but 2008–2009 reservoir elevation was not (P < 0.05). The amplitude of forebay elevation fluctuations was greater during fall/winter (November–March) and early spring, and less during summer (July–September). The mean daily tailrace elevation downstream of each dam was significantly higher in 2010–2011 than in 2008–2009 (P < 0.001; Figure 4.2; USACE 2011). When forebay elevations decreased in late spring because of operation at minimum operating pool (MOP) and increased spill operations at the dams, tailrace elevation increased. This change in elevation signature was less pronounced at Little Goose Dam that at others but was nonetheless significant (P < 0.001). The increase in tailwater elevation not only was greater during 2010–2011 but it lasted longer, dropping around July 26 rather than July 6 (2008–2009).

In general, temperatures recorded in the forebay and tailrace areas of dam projects on the lower Snake River were similar to each other. During 2010–2011, mean daily forebay reservoir temperatures were markedly lower throughout spring and early summer than both those recorded in 2008–2009, and 10-year average temperatures recorded for 2001–2010 (Figure 4.3; UW 2011). Mean daily forebay temperatures in 2010–2011 were significantly lower than 10-year averages in all reservoirs and—with the exception of Lower Granite—significantly lower than 2008–2009 averages (P < 0.05). These protracted, unseasonably low temperatures lasted until August 1. Mean daily forebay temperatures in 2010–2011 peaked at 21.1°C in Ice Harbor Reservoir. Likewise, in previous years, highest mean daily forebay temperatures were found in mid-August in the Ice Harbor impoundment (21.8°C). Data recorded during fall/winter by the Columbia River Data Access in Real Time service are sparse but indicate that temperatures during this season were similar to the 10-year average (UW 2011).

4.1

4.2

Final Repor Figure 4.1. Mean daily forebay elevation (ft) in (A) Lower Granite, (B) Little Goose, (C) Lower Monumental, and (D) Ice Harbor reservoirs over the 2010–2011 study period, compared with the 2008–2009 and 2001–2010 mean daily reservoir elevations. Mean daily reservoir elevation for 2008–2009 and 2010–2011 was significantly lower than the 10-year average, 2001-10 (P < 0.05). Fluctuations in fall/winter and late summer were greater than those during spring and early summer. t

4.3

Final Repor Figure 4.2. Mean daily elevation (ft) in the tailrace of (A) Lower Granite, (B) Little Goose, (C) Lower Monumental, and (D) Ice Harbor dams over the 2010–2011 study period, compared with 2008–2009. Mean daily tailrace elevation for 2008–2009 was significantly lower than that for 2010–2011 (P < 0.05). t

4.4

Figure 4.3. Mean daily reservoir temperature (°C) in (A) Lower Granite, (B) Little Goose, (C) Lower Monumental, and (D) Ice Harbor reservoirs Final Repor over the 2010–2011 study period, compared with the 2008–2009 and 2001–2010 mean daily reservoir temperatures. Late spring and early summer temperatures were much lower during spring/summer 2011. t

4.5

Figure 4.4. Mean daily reservoir discharge (kcfs) in (A) Lower Granite, (B) Little Goose, (C) Lower Monumental, and (D) Ice Harbor reservoirs during 2010–2011, compared to the 2008–2009 and 2001–2010 mean daily reservoir discharges. During 2010–2011, discharges were

higher and lasted longer than during previous years. Final Repor t

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Final Repor Figure 4.5. Mean daily percentage saturation of TDG at lower Snake River reservoirs during 2010–2011 and 2008–2009. t

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Figure 4.6. Mean daily reservoir spill (kcfs) in (A) Lower Granite, (B) Little Goose, (C) Lower Monumental, and (D) Ice Harbor reservoirs over the 2010–2011 study period, compared with the 2008–2009 and 2001–2010 mean daily spill. The volume of water spilled was Final Repor relatively high during 2011.

t

Final Report

Temperatures were unseasonably low due to comparatively high mean daily discharges from January through September 2010–2011. Discharge in 2010–2011 was significantly higher than mean daily discharges in 2008–2009 and 2001–2010 (P < 0.05; UW 2011). Peak mean daily discharges not only were higher but also lasted longer, from mid-May through July, in 2010–2011 than in previous years (Figure 4.4). Overall, the percentage saturation of total dissolved gas (TDG) was higher during 2010–2011, although for all four lower Snake River reservoirs combined, this difference was not significant (P = 0.213; Figure 4.5; USACE 2011). However, the difference was significant within Lower Granite and Little Goose reservoirs (P < 0.002), where TDG measurements reached 135% on May 26 in the Little Goose impoundment. Percentage saturation of TDG was 2%–4% higher during 2010–2011 than during 2008–2009.

Spill operations during 2010–2011 were conducted at approximately the same time as previous years (mid-April through mid-July) at Lower Granite, Little Goose, Lower Monumental, and Ice Harbor dams (Figure 4.6). However, mean daily spill was significantly greater through these months during 2010–2011 than during 2008–2009 or 2001–2010.

4.2 Fish Species Composition, Abundance, and Habitat Use

A total of 18,676 fish representing 31 different species were caught or observed during electrofishing, seining, and snorkeling efforts between January 2011 and September 2011 (Appendix C, Tables C.1–C.3). The greatest number of fish were sampled via seining (n = 6,693), followed by electrofishing (n = 6,151) and snorkeling (n=5,832). The greatest number of fish were sampled in Ice Harbor Reservoir (n = 7,221), and the fewest fish were sampled in Little Goose Reservoir (n = 1,682). The sites where the most fish were sampled included Tucannon River Upper (n = 2,185), Devil’s Bench Upper (n = 1,187), Burr Canyon Upper (n = 1,409), Burr Canyon Lower (n = 1,966), and Burr Shoal Upper (n = 2,024). The fewest number of fish were found at New York Island Lower (n = 104), Tucannon River Lower (n = 178), and New York Island Upper (n = 184).

4.2.1 Salmonid Distribution

The majority of juvenile Chinook salmon were sampled during the spring (April–June; Figure 4.7) from sites upstream of Little Goose Dam (Figure 4.8). Of the 2,648 juvenile Chinook salmon sampled by seining and electrofishing, 83% were sampled from Lower Granite Reservoir and tailrace (Figure 4.8). Using electrofishing, we sampled 500 Chinook salmon at Knoxway Bay during the spring and 375 at the Clarkston site during mid-April. In addition, a minimum of 160 Chinook salmon were caught at each of Knoxway Bench Lower, Knoxway Bay Lower, Offield Landing Upper, and Illia Dunes Upper sites during late May and June via seining. Using seining, we found less than 10 Chinook salmon over the entire season at other locations (Asotin Slough, Illia Dunes Lower, New York Island Lower, Burr Canyon, Burr Shoal Lower, and Sheffler Shoal Lower). No Chinook salmon were seen during snorkeling efforts; however, we were not able to snorkel during the spring (April–June) due to high turbidity and resultant low visibility. Other species of salmonids collected included coho salmon (Oncorhynchus kisutch), steelhead (Oncorhynchus mykiss), and mountain whitefish (Prosopium williamsoni). Thirty-four juvenile coho salmon (47 to 260 mm) were sampled during the study period throughout all reservoirs in the lower Snake River. Five adult steelhead were found (one at each site unless otherwise noted) at Offield Landing Upper (June 25, 2011), Tucannon River Upper (one each on April 26 and June 8, 2011, Burr Shoal Lower (May 19, 2011), and Sheffler Shoal Lower (April 21, 2011).

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A total of 195 mountain whitefish were sampled, the majority (n = 152) of which were caught at Asotin Slough from January through May.

A) Seining B) Electrofishing Winter Spring Summer Winter Spring 1200 1800 1600 1000 1400 800 1200 1000 600 800

400 CPUE / 600 s 600 400

Number of of Found Fish Number 200 200 0 0 Chinook Coho Mountain Rainbow Sockeye Steelhead Chinook Coho Salmon Mountain Steelhead Salmon Salmon Whitefish Trout Salmon Salmon Salmon Whitefish Figure 4.7. Number of salmonids sampled by season using seining (A) and electrofishing (B). Winter sampling occurred in January. No salmonids were found during snorkeling efforts, which were not conducted during the spring (April–June) due to high turbidity and associated low visibility. Electrofishing was not conducted during summer (July–September) due to water temperatures that exceeded the allowances of our federal collection permit.

SEINING ELECTROFISHING 1200

1000

800

600

400

200 Total Number of Chinook Salmon Found Total

0 ASOTIN LGR LGS LMN IHR Pool

Figure 4.8. Number of Chinook salmon found in each pool by seining and electrofishing. Electrofishing was not conducted during summer (July–September) due to water temperatures that exceeded the allowances of our federal collection permit.

We classified all juvenile Chinook salmon captured according to adult run timing based on their length and date of capture (Table 4.1; Figure 4.9; Appendix C, Figures C.1–C.24). This classification scheme was developed based on passive integrated transponder tag passage data at Lower Granite Dam (PTAGIS 2011), timing of upstream hatchery releases (Fish Passage Center 2011), and previous research

4.9 Final Report conducted on the Snake River (Connor et al. 2005; Seybold and Bennett 2010). Electrofishing caught many more spring/summer Chinook salmon yearlings (n = 1,115 versus n = 213) and fall reservoir-type Chinook salmon yearlings (n = 102 versus n = 1) than seining. However, seining was much more effective at sampling fall Chinook salmon subyearlings (n = 951) than was electrofishing (n = 247; Figure 4.9). Similar numbers of spring Chinook salmon subyearlings were captured seining (n = 9) and electrofishing (n = 10).

Table 4.1. Dates and sizes of catch used to identify Chinook salmon runs. Date Size Classification January <170 mm Spring Chinook salmon subyearlings >170 mm Fall reservoir-type Chinook salmon yearlings First week of April <80 mm Spring Chinook salmon subyearlings <170 mm Spring Chinook salmon yearlings >170 mm Fall reservoir-type Chinook salmon yearlings Third week of April <80 mm Spring Chinook salmon subyearlings <185 mm Spring Chinook salmon yearlings >185 mm Fall reservoir-type Chinook salmon yearlings May <110 mm Fall ocean-type Chinook salmon subyearlings <200 mm Spring Chinook salmon yearlings >200 mm Fall reservoir-type Chinook salmon yearlings June <120 mm Fall ocean-type Chinook salmon subyearlings >120 mm Spring Chinook salmon yearlings

SEINING ELECTROFISHING 1200

1000

800

600

400

200 Total Number of Total Chinook Salmon Found

0 Spring subyearling Fall, ocean-type, Spring yearling Fall, reservoir-type, subyearling yearling Chinook Salmon Run

Figure 4.9. Chinook salmon categorized into different run types. Electrofishing was not conducted during summer (July–September) due to water temperatures that exceeded the allowances of our federal collection permit.

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Types of fish sampled during electrofishing and seining surveys at Knoxway Bench Upper (unmodified, with a steep lateral bed slope) and Lower (modified, with a shallow lateral bed slope) were generally similar. However, ocean-type fall Chinook salmon subyearlings appeared to prefer the shallower habitat of Knoxway Bench Lower. During spring seining, significantly more ocean-type fall Chinook salmon subyearlings were found at Knoxway Bench Lower (n = 208) than at Knoxway Bench Upper (n = 77; P = 0.022). Fairly equal numbers of Chinook salmon were electrofished from the two sites (n = 86 for Upper and n = 64 for Lower), with no significant difference between the two sites (P > 0.05)

The best-fitting NPMR models showed that the highest electrofishing CPUE (for all juvenile Chinook salmon) occurred upstream of rkm 120 (Figure 4.10; xR2 = 0.49), and the highest seining CPUE (for subyearling fall Chinook salmon) occurred between rkm 120 and 230, which corresponds to New York Island upstream to Clarkston (Figure 4.11; xR2 = 0.71).

Figure 4.10. NPMR projection graph depicting the relationship between electrofishing CPUE of juvenile Chinook salmon (CHefish), river kilometer (rkm), and percentage gravel in dredge samples (Gravel). Figure is oriented to display the relationship between CPUE and rkm.

Figure 4.11. NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon (CH0seine), river kilometer (rkm), and percentage gravel in dredge samples (Gravel).

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Despite significantly higher discharge and spill during 2010–2011 compared to 2008–2009, the spatial distribution of salmonids was generally similar during both periods (Seybold and Bennett 2010). Previous seining efforts resulted in larger numbers of spring Chinook salmon yearlings (Seybold and Bennett 2010); however, we caught proportionately more fall Chinook salmon subyearlings. Previously, yearling spring Chinook salmon were the most abundant at Knoxway Bench Upper and Lower, in contrast with our study, where only 4% of the Chinook salmon caught at Knoxway Bench were spring yearling Chinook salmon.

4.2.2 Non-Salmonid Fish Community

Most piscivorous fish were sampled during the spring (Figure 4.12). Of the 437 predator-size fish that were caught, the majority (>85%) were northern pikeminnow and smallmouth bass (Figures 4.12 and 4.13 and Appendix C, Tables C.2 and C.3; Figures C.25–C.48). However, small numbers of channel catfish (Ictalurus punctatus), black crappie (Pomoxis nigromaculatus), white crappie (Pomoxis annularis), yellow and brown bullheads (Ameiurus natalis and Ameiurus nebulosus), bull trout, yellow perch (Perca flavescens), and walleye (Sander vitreus) were also caught. We did not encounter any largemouth bass during seining or electrofishing, but seven were observed during summer snorkeling.

Fifty percent of all predators were caught at Clarkston, Knoxway Bench, Knoxway Bay, Offield Landing, and Illia Dunes (sites where Chinook salmon were also present). Smallmouth bass were the most frequently captured predator in the Lower Granite, Little Goose, and Lower Monumental reservoirs (75% of 275). In Ice Harbor Reservoir, numbers of northern pikeminnow and smallmouth bass were similar (Figure 4.13). This varies from previous research, when northern pikeminnow were most abundant in Ice Harbor Reservoir (Sebyold and Bennett 2010). Significant differences in number of predators between pools, sites, and types of sites were not common. More smallmouth bass were sampled during electrofishing surveys at Knoxway Bench Upper (n = 28) than at Knoxway Bench Lower (n = 18); however, the difference was not significant (P > 0.05).

A) Seining - Predator-size B) Electrofishing - Predator-size Winter Spring Summer Winter Spring 300 16 250 14 200 12 150 10 100

8 CPUE / 600 s 6 50 4 0 2 Total Number of Fish FoundNumber of Fish Total 0 Black Channel Northern Smallmouth Yellow Perch Crappie Catfish Pikeminnow Bass Figure 4.12. Seasonal distribution of predator-size fish for seining (A) and electrofishing (B).

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SEINING ELECTROFISHING 250 SMB = 166 200 NPM = 19

150 SMB = 57 NPM = 56 100 SMB = 25 50 SMB = 15 NPM = 9 SMB = 1 NPM = 8

Total Number of Predators Found of PredatorsNumber Total NPM = 5 0 ASOTIN LGR LGS LMN IHR Pool

Figure 4.13. Total number of predator-size fish found in each pool for seining and electrofishing. The number of smallmouth bass (SMB) and northern pikeminnow (NPM) found during electrofishing in each pool is noted in text above the red bar.

Stomach contents from smallmouth bass collected during spring electrofishing indicated that signal crayfish (Pacifastacus leniusculus) formed two-thirds of the diet by weight. By weight, fish formed roughly one-third of the diet. Of the fish prey consumed by smallmouth bass, sandrollers (Percopsis transmontana) were the most common item, followed by peamouth (Mylocheilus caurinus) and chiselmouth (Acrocheilus alutaceus). Sandrollers were found only in the stomachs of smallmouth bass from Ice Harbor and Lower Granite reservoirs. Chinook salmon and other unidentified salmonids formed 6% of the diet by weight. The low rate of predation on salmonids has been found in other studies of the Snake River (e.g., Tabor et al 1993; Naughton et al 2004). The most recent study, Seybold and Bennett (2010), found very little evidence of smallmouth bass predation on Chinook salmon.

Only one bull trout was sampled during this study; it was captured while electrofishing on April 22, 2011, at Tucannon River Upper. Previously, a bull trout was found at Tucannon River Lower in February (Seybold and Bennett 2010). There is an established population of bull trout in the Tucannon River (Underwood et al. 1995; Dunham et al. 2003), and bull trout have been observed at the fish-viewing windows during spring and summer at Lower Monumental and Little Goose dams and at the adult/ juvenile separator at Little Goose Dam (Faler et al. 2004). It is thought that the Tucannon River bull trout populations are utilizing the Snake River for over-wintering habitat (Faler et al. 2004).

High numbers of juvenile northern pikeminnow and smallmouth bass were present during the summer based on seining and snorkeling (Figure 4.14). However, very few of these fish were large enough to be considered piscivorous (Seybold and Bennett 2010). About 75% of the 3,418 juvenile smallmouth bass observed during summer snorkeling occurred at Tucannon River Upper, Devil’s Bench Upper and Lower, and at Burr Shoal Lower. Juvenile predator species were generally found in the same areas as those of the adult life stage.

4.13 Final Report

A) Seining - Juvenile Predators B) Electrofishing - Juvenile Predators Winter Spring Summer Winter Spring 35 900 800 30 700 25

600 20 500 15 400 CPUE / 600 s 300 10 200 5

TotalNumber 100 of FishFound 0 0 Northern Smallmouth Walleye Yellow Perch Northern Pikeminnow Smallmouth Bass Pikeminnow Bass Figure 4.14. Seasonal distribution of juvenile-size predator fish species for seining (A) and electrofishing (B).

Numerous peamouth (n = 4,657), largescale sucker (Catostomus macrocheilus; n = 2,093), sandroller (n = 493), bridgelip sucker (Catostomus columbianus; n = 249), and redside shiner (Richardsonius balteatus; n = 228) were sampled during seining and electrofishing (Appendix C, Tables C.2 and C.3). Most peamouth were sampled in the Ice Harbor pool and in the backwater environments of Knoxway Bay Lower and Illia Dunes Lower during late May and early August. Largescale suckers were captured from most sites during electrofishing surveys; those captured in seines occurred primarily at Burr Canyon Lower and Burr Shoal Upper. Sandrollers were most abundant at Illia Dunes in the spring. American shad and redside shiner were sampled more frequently during the summer (Appendix C, Figures C.49 and C.50). In addition, large numbers of juveniles were observed by snorkelers in late summer, including 1,105 pumpkinseeds (Lepomis gibbosus; Tucannon River Upper) and 817 American shad (Burr Canyon Upper and Lower). We did not encounter any longnose dace (Rhinichthys cataractae), speckled dace (Rhinichthys osculus), or fathead minnows (Pimephales promelas), which were seen during previous research at the same sites in 2009 (Seybold and Bennett 2010).

4.2.3 Determination of Pacific Lamprey Presence/Absence

Prior to conducting field surveys for juvenile Pacific lamprey, we tested the effectiveness of a new shocking method under controlled laboratory conditions.

4.2.3.1 Laboratory Test to Evaluate New Sampling Method

Of the 30 lampreys released, the majority (n = 23; 76%) burrowed into the substrate within approximately 15 cm of the edge of the pen (Mueller et al. in press). The remaining 7 burrowed near the center of the pen within the rectangular region encompassed by the four electrodes. Within this region, the average voltage was 0.38 V/cm while the average voltage outside this region was 0.30 V/cm. Of those that burrowed outside the center region, only 11 (48%) were induced to emerge by shocking; whereas 86% (6 of 7) of those that burrowed in or very near the center region were induced to emerge. The number of lamprey induced to emerge ranged from 4 to 7 for the three tests. The mean detection rate for the three individual trials was 60% (SD = 15.2%). Of the 17 lampreys that emerged, 13 emerged within 5 cm and 4 emerged within 13 cm from where they originally burrowed. The interval between initiation of shocking and the time at which the first lamprey became visible was fairly short. Of the

4.14 Final Report

17 lampreys that emerged, the majority (89%) emerged within the first 5 s of shocking. Of those that did not emerge within 5 s, the longest time to emergence was 13 s. One mortality was recorded 48 h after testing. The capture technique post-testing required the tanks to be drained and all sediment sifted to collect any remaining lamprey; this procedure likely resulted in the single post-test mortality.

4.2.3.2 Field Searches for Pacific Lamprey

No juvenile lamprey were found during searches conducted in July and September 2011. Maps showing the detailed location of each survey are included in Appendix A. The total sampling area shocked during each sampling trip was approximately 300 m2. Visibility during 2011 was affected by low water clarity due to the high volume and protracted nature of the spring discharge. Turbidity ranged from 3–7 NTU during lamprey searches in late July and improved to 3–5 NTU during late September (Appendix C, Table C.4). Based on the laboratory tests conducted for this study and previous underwater video surveys, a turbidity value of 4 NTU or less is recommended when conducting video-based searches in the lower Snake River (Dauble et al. 1999).

Although we did not observe lamprey ammocoetes or macrothalma during late summer surveys, our sampling area covered only a small fraction of the total region that could represent suitable rearing habitat. Juvenile lamprey are typically found in silt/sand substrate but have a patchy distribution related to other environmental variables such as water depth and velocity, light level, organic content, chlorophyll concentration, proximity to spawning area and riparian canopy (Moser et al. 2007). Many of our survey sites had a silt/sand matrix and thus appeared to be suitable habitat. The extent to which juvenile lamprey utilize the lower Snake River for rearing is unknown. However, larval lamprey were reported within exposed mud flats in the Lower Granite tailrace during a test reservoir drawdown (Dauble and Giest 1992). In addition, a translocation program released adult lamprey in Asotin Creek from 2007 to 2009; five redds were documented there in 2008. Pacific lamprey have also been documented in the Tucannon River (USFWS 2010).

Identification of available spawning and rearing habitat for Pacific lamprey in lower Snake River reservoirs is not possible without a comprehensive substrate survey of the lower Snake River. Based on findings of deepwater dredging surveys in the lower Columbia River (Jolley et al. 2010), future substrate surveys should be prioritized in dam tailrace areas and near the mouths of tributary streams.

4.3 Taxonomic Composition and Abundance of Zooplankton, Phytoplankton, and Periphyton

4.3.1 Zooplankton

From January through September 2011, approximately 168 zooplankton samples were collected at the 24 sample sites (Appendix D). Zooplankton were most abundant during spring (April through June), with 27,051 individuals collected. The majority of these individuals (25,519, or 94.3%) belonged to the phylum Rotifera. Seasonally, the three most numerically abundant taxa were phylum Rotifera, subclass Copepoda, and genus Bosmina during fall/winter (January); phylum Rotifera, subclass Copepoda, and order Cyclopoida during spring; and phylum Rotifera, subclass Copepoda, and genus Daphnia during summer (July through September). Taxa richness increased seasonally, with 9 distinct genera identified during fall/winter, 19 identified during spring, and 24 identified during summer.

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Zooplankton densities ranged from 0.08 to 2.08 individuals/L and were distributed fairly evenly across all locations, although they were highest at Knoxway Bench (with no difference between the modified lower transect and the unmodified upper transect). Previous studies of similar scale conducted on the lower Snake and mid-Columbia rivers reported comparable mean densities of 0.02 to 5.00 individuals/L (Harris 1979; Rondorf et al. 1990; Seybold and Bennett 2010).

Generally, zooplankton densities did not differ significantly among sites, transects, or reservoirs. Mean spring densities were slightly higher where Chinook salmon were found than at sites where they were not found, but these differences were not significant (Figure 4.15). Zooplankton density tended to be highest in main-stem reservoir locations with a gradual lateral bed slope and lowest in free-flowing reaches (Asotin Slough); this difference was significant at a 94% confidence interval (P = 0.054). Such a difference may arise from gear bias. The Wisconsin-style plankton net used to capture zooplankton densities distributed vertically in the water column was less effective in the presence of swift currents that prevailed at Asotin Slough. Densities found at each site during spring were significantly higher than fall/winter and summer densities (P < 0.05). This trend is evident within Lower Granite Reservoir, for example (Figure 4.16).

1.2 Lower Granite Little Lower Ice Harbor Goose Monumental 1.0

0.8

0.6

0.4

0.2 Mean Zooplankton Density/ (Individuals L) 0.0

83% of Chinook found here Transect

Figure 4.15. Mean zooplankton densities (individuals/L) measured per site throughout the study period. There was no significant difference between transects within study sites.

Zooplankton densities were not strongly correlated to Chinook salmon CPUE, although some peaks and valleys in the data align in the Lower Granite impoundment (R = 0.15; Figure 4.17). Among zooplankton taxa, Daphnia have been documented as a particularly important cladoceran food item for juvenile Chinook salmon in the lower Snake and mid-Columbia rivers (Becker 1971; Edwards et al. 1974; Harris 1979; Rondorf et al. 1990; Haskell et al. 2006). Studies have further shown that Daphnia can “bloom” within these systems during late summer (July–September), when the zooplankter can thereby assume numerical and volumetric importance in the diet of subyearling Chinook salmon and other, maturing fishes (Dauble et al. 1980; Mehner 2000; Seybold and Bennett 2010). While other zooplankton

4.16 Final Report taxa were relatively most abundant in spring, Daphnia were identified in notable numbers during September sampling only. Daphnia were most abundant in the Ice Harbor impoundment, making up more than 50% of a sample taken from Sheffler Shoal in September (Figure 4.18). Relatively high abundances of Daphnia downstream from sites occupied by salmon may also indicate greater planktonivory by either Chinook salmon or predator species at those sites (Mehner 2000).

1.6

1.4

1.2

1.0

0.8 Fall / Winter Spring 0.6 Summer

0.4

Mean Zooplankton / L) Density (Individuals 0.2

0.0 Asotin Slough Clarkston Knoxway Bench Knoxway Bay Offield Landing Transect

Figure 4.16. Mean zooplankton densities (individuals/L) measured per season in Lower Granite Reservoir locations. Spring zooplankton densities were significantly greater than fall/winter and summer zooplankton densities (P < 0.05).

Overall Mean Chinook Overall Mean Zooplankton Density 300.0 Lower Granite Little Lower Ice Harbor 1.2 Goose Monumental

250.0 1.0

200.0 0.8

150.0 0.6

100.0 0.4 Chinook (Catch per Unit Effort) 50.0 0.2 Zoolplankton Density ( Individuals / L)

0.0 0.0 Illia L Illia U Asotin L Asotin Offield L Offield Asotin U Asotin Burr Sh L Burr Ca L Offield U Offield Sheffler L Sheffler Burr Sh U Burr Ca U Sheffler U Sheffler Knox Bay L Bay Knox NY Island L Island NY Clarkston L Clarkston Knox Bay U Knox Bay NY Island U Island NY Tucannon L Tucannon Clarkston U Clarkston Tucannon U Tucannon Dev Bench L Dev Bench Dev U Bench Knox L Bench Knox U Bench Site

Figure 4.17. Overall mean Chinook salmon (CPUE) sampled via electrofishing and overall mean zooplankton densities (individuals/L) per transect.

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60.0% Lower Granite Little Goose Lower Ice Harbor Monumental 50.0% Daphnia 40.0%

30.0%

20.0%

10.0% Mean Relative Abundance of of Abundance Relative Mean

0.0%

Site 83% of Chinookfound here

Figure 4.18. Relative abundance of Daphnia found during September, the only month during which Daphnia were identified in notable quantities.

Seybold and Bennett (2010) reported Daphnia throughout the year, although their densities also peaked in September. This late- summer increase may result from decreased turbidity and increased primary production in the Snake River during that month; Daphnia are sensitive to suspended silt and fine sediments, which have been shown to interfere with mechanical collection and ingestion of food in turbid reservoir environments (Arruda et al. 1983; Kirk 1992). Indeed, percentage silt gathered from the benthos is relatively low at Ice Harbor sites, where most Daphnia were found (Figure 4.19). Burr Canyon Upper was the exception, with greater than 15% silt/fines (<0.063 mm) where relative abundance of Daphnia was low. The presence of Daphnia has also been shown to increase with organic carbon throughout the water column (Strom et al. 1997; Carpenter et al. 1998). In our study, however, this relationship was not strong. Overall, zooplankton density was positively correlated to percentage organic carbon (benthic) by site, but this relationship was also weak (R = 0.26).

4.3.2 Phytoplankton and Periphyton

Mean phytoplankton densities were fairly uniform across all 24 transects (110–120 individuals/L) and were not limiting to zooplankton densities (individuals/L; Figure 4.20). Although mean phytoplankton densities did not vary greatly among seasons (110–130 individuals/L), they were significantly lower in fall/winter than in spring and summer for all reservoirs (P < 0.05). For example, this trend is evident within Lower Granite Reservoir (Figure 4.21). Full summary data are available in Appendix D.

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Daphnia's Relative Abundance % silt / fines (<0.063 mm) % organic C 25.0 25 Lower Granite Little Lower Ice Harbor Goose Monumental

20.0 20 Daphnia

15.0 15

10.0 10

5.0 5 Percentageof Silt / Fines and Organic C Mean Relative of Abundance

0.0 0

Site

Figure 4.19. Relative abundance of Daphnia, percentage silt and fines, and percentage organic carbon measured per transect throughout the study period.

Phytoplankton Zooplankton 140.0 1.2 Lower Granite Little Lower Ice Harbor Goose Monumental 120.0 1.0

100.0 0.8 80.0 0.6 60.0 0.4 40.0

20.0 0.2

0.0 0.0 L) / (Individuals Density Zooplankton Mean Mean Phytoplankton Density (Individuals / L) / (Individuals Density Phytoplankton Mean

83% of Chinookfound here Transect

Figure 4.20. Mean phytoplankton and zooplankton densities (individuals/L) measured per site throughout the study period. There was no significant difference between transects (upper and lower sample sites). There were no significant differences between sample sites where salmonids were found versus other locations.

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140.0

120.0

100.0

80.0 Fall / Winter 60.0 Spring Summer 40.0

20.0 Mean Phytoplankton Density (Individuals / L) / (Individuals Density Phytoplankton Mean

0.0 Asotin Slough Clarkston Knoxway Bench Knoxway Bay Offield Landing Transect

Figure 4.21. Mean phytoplankton densities (individuals/L) measured seasonally in Lower Granite Reservoir locations. Fall/winter phytoplankton densities were significantly lower than summer (P < 0.05).

As expected, mean phytoplankton biomass (g) was congruent to mean chlorophyll a content (g/L), neither of which varied appreciably across all 24 study sites (Figure 4.22). There were no significant differences between sample sites where salmonids were found and other locations (Figure 4.22). Seasonally, however, spring biomasses and chlorophyll a contents were significantly greater than those recorded for fall/winter and summer (P < 0.05; Figures 4.23 and 4.24). Although Makarewicz and Bertram (1991) and Seybold and Bennett (2010) verify what is commonly regarded as a canonical biomass and chlorophyll a peak in late spring and early summer, this does not account for comparatively higher mean phytoplankton biomass and chlorophyll a content found during the fall/winter months than the summer in 2010–2011. As Winder and Cloern (2010) explain, spring blooms often last 2 weeks to 2 months; nutrient limitation, grazing, and cell sinking eventually cause them to contract or collapse. However, a secondary phytoplankton biomass peak can occur in autumn due to excess nutrients (Sommer et al. 1986; Winder and Cloern 2010). It is possible that disposition of windblown topsoil and nutrients released following wheat harvests in the Palouse hills surrounding the Snake River contributed to such a bloom.

Mean periphyton biomass (g) collected from artificial substrates in nearshore areas varied more than phytoplankton biomass across the 24 sample sites (Figure 4.25). However, this variation was not significant, nor did it follow any pattern among unmodified and modified sites or sites where Chinook salmon were found and sites where they were not, although it did tend to increase slightly in a downstream direction. Periphyton chlorophyll a content was strongly correlated with biomass (R = 1.00; Figure 4.25). Both mean biomass and chlorophyll a content were significantly higher during the summer months (P < 0.05; Figures 4.26 and 4.27). This may be attributed to increasing hours of daylight and decreasing turbidity as the year progressed (through September), leading to greater photic exposure of benthic areas.

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Biomass Chlorophyll a

0.08 Lower Granite Little Lower Ice Harbor 0.0012 Goose Monumental 0.07 0.0010 0.06 0.0008 0.05

0.04 0.0006

0.03 0.0004 0.02 Mean Chlorophyll a (g / L) 0.0002 Mean Phytoplankton (g) Biomass 0.01

0.00 0.0000

83% of Chinookfound here Transect

Figure 4.22. Mean phytoplankton biomasses (g) and chlorophyll a content (individuals/L) measured per site throughout the study period. Chlorophyll a tends to increase and decrease with biomass.

0.10 Little Goose Lower Monumental 0.09

0.08

0.07

0.06

0.05 Fall / Winter Spring 0.04 Summer 0.03 Mean Phytoplankton Biomass (g) Biomass Phytoplankton Mean 0.02

0.01

0.00 Illia Dunes New York Island Tucannon River Devil's Bench Transect

Figure 4.23. Mean phytoplankton biomasses (g) measured per site per season in Little Goose and Lower Monumental reservoirs. Summer phytoplankton biomasses (g) were significantly lower than spring and fall/winter.

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0.0014 Little Goose Lower Monumental

0.0012

0.0010

0.0008 Fall / Winter 0.0006 Spring Summer 0.0004

Mean Phytoplankton Chlorophyll a (g / L) / (g a Chlorophyll Phytoplankton Mean 0.0002

0.0000 Illia Dunes New York Island Tucannon River Devil's Bench Transect

Figure 4.24. Mean phytoplankton chlorophyll a content (g/L) measured per site per season in Little Goose and Lower Monumental reservoirs. Summer phytoplankton chlorophyll a contents (g/L) were significantly lower than spring and fall/winter (P < 0.05).

Biomass Chlorophyll a 0.08 Lower Granite Little Lower Ice Harbor 0.0012 Goose Monumental 0.07 0.0010 0.06 0.0008 0.05 0.04 0.0006 0.03 0.0004 0.02 0.0002 0.01 Mean Chlorophyll(gL) a / Mean Periphyton Biomass (g) Biomass Periphyton Mean 0.00 0.0000

Transect

Figure 4.25. Mean periphyton biomasses (g) and chlorophyll a content (individuals/L) measured per site throughout the study period. Chlorophyll a tends to increase and decrease with biomass. There was no significant difference between transects (upper and lower sample sites). There were no significant differences between sample sites where salmonids were found and other locations.

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0.10

0.09

0.08

0.07

0.06

0.05 Fall / Winter 0.04 Summer 0.03

Mean Periphyton Biomass (g) Biomass Periphyton Mean 0.02

0.01

0.00 Burr Canyon Burr Shoal Sheffler Shoal Transect

Figure 4.26. Mean periphyton biomasses (g) measured per site per season in Ice Harbor Reservoir. Fall/winter periphyton biomasses (g) were significantly lower than summer (P < 0.05).

0.0016

0.0014

0.0012

0.0010

0.0008 Fall / Winter 0.0006 Summer

0.0004

Mean Periphyton a (g Chlorophyll / L) 0.0002

0.0000 Burr Canyon Burr Shoal Sheffler Shoal Transect

Figure 4.27. Mean periphyton chlorophyll a (g/L) measured per site per season in Ice Harbor Reservoir. Fall/winter periphyton chlorophyll a contents (g/L) were significantly lower than summer (P < 0.05).

4.4 Macroinvertebrate Distribution and Abundance

Representatives from 76 distinct genera of benthic macroinvertebrates were sampled using a variety of methods (rock baskets, kick net, and Ponar dredge), each of which were employed to measure abundance at multiple depths along each transect (Table 4.2). Rock baskets proved successful in collecting macroinvertebrates; by comparison, the relative contribution to the total collected from kick-net and Ponar dredge samples was negligible. Kick-net sampling is more effective where flowing water

4.23 Final Report deposits dislodged organisms into the net (Barbour et al. 1999). In our nearshore sampling environment, flows were often minimal or changed direction due to eddy currents. The Ponar dredge was not effective at sampling coarse or embedded sediments.

Table 4.2. Macroinvertebrate taxa collected from 24 sample sites throughout Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs during the November 2010–September 2011 sampling period. Class Order Family Hydrophilidae Elmidae Coleoptera (Beetles) Carabidae Hydrophilidae Psephenidae Chironomidae Culicidae Diptera (Flies) Psychodidae Stratiomyidae Baetidae Caenidae Ephemerellidae Ephemeroptera(Mayflies) Ephemeridae Heptageniidae Insecta Potomanthidae Gomphidae Odonata (Dragonflies) Lestidae Chloroperlidae Plecoptera (Stoneflies) Pteronarcyidae Nemouridae Brachycentridae Helicopsychidae Hydropsychidae Hydroptilidae Trichoptera (Caddisflies) Limnephilidae Polycentropodidae Uenoidae Lepidostomatidae Corophiidae Amphipoda (Scuds) Gammaridae Malacostraca Isopoda Asellidae Decapoda (Crayfish) Astacidae Veneroida (Bivalve Molluscs) Corbicula Bivalvia Unionidae Unionoida (Bivalve Molluscs) Sphaeriidae Bithyniidae Sorbeoconcha (Snails) Pleuroceridae Lymnaeidae Gastropoda Physidae Basommatophora (Snails) Planorbidae Ancylidae Oligochaeta (Annelid Worms) Unclassified Unclassified Polychaeta (Annelid Worms) Unclassified Unclassified

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Numerical abundance and taxa richness generally increased throughout the November 2010– September 2011 sampling period. Full summary tables are included in Appendix E. During summer (June–September), 32 genera were sampled, the most numerous of which belonged to the families Chironomidae, Corophiidae, Gammaridae, and class Oligochaeta. These genera were the most prolific throughout the study. Twenty-eight and 20 genera were identified in the fall/winter and spring months, respectively. Six Ephemeroptera families were found, including representatives of the family Potomanthidae at Devil’s Bench Upper and Burr Canyon Lower, which is unusual for the region (McCafferty 1998). Because this taxa is particularly sensitive to disturbance and contamination, the presence of Potomanthidae suggests increased habitat quality rather than degradation (Merrit and Cummins 1996). A photograph of a Potomanthidae specimen is included in Appendix E. In addition, a specimen of Ripistes parasita (class Oligochaeta, order Haplotaxida, family Naididae) was discovered at Tucannon Upper in July, a Eurasian exotic previously undocumented in the Snake River. This non-native Oligochaete spread to the United States via shipping, where it was found inhabiting varied habitat as early as 1984 in New York, Minnesota, and the Great Lakes region (Simpson and Abele 1984; Montz 1988; USGS 2011). Because Tucannon Upper is located approximately 50 m from the main shipping channel, it is likely that Ripistes parasita was introduced to the Snake River by similar means.

Habitat quality relative to benthic macroinvertebrates was assessed at each of the 24 sample sites using three macroinvertebrate indices: 1) biomass, 2) relative abundance, and 3) Shannon’s Diversity Index. Specifically, biomass and relative abundance analyses were focused on the orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), with the addition of the order Diptera (DEPT). Both Shannon’s Diversity Index and EPT were used as overall indicators of water quality, while DEPT was used as an indicator of the biomass and relative abundance of important food sources for juvenile salmonids (Becker 1970, 1971; Edwards et al. 1974; Schreffler et al. 1992; Curet 1993; Merritt and Cummins 1996; Bennett 1997a; Angradi 1999; Stark 2001; Cover et al. 2008; Seybold and Bennett 2010).

As members of these indices, Plecoptera were scarce. This scarcity may, itself, be an indicator of a pre-impoundment to impoundment shift, from lotic to more lentic conditions, because historical, pre-dam accounts on the mid-Columbia and lower Snake Rivers report numerous stonefly (Plecoptera) genera (Stark 2001). Mean biomass of all genera collected did not vary from among sites, reservoirs, or rock types (alluvium versus angular colluvium).

4.4.1 EPT Index

Mean EPT biomass (mg) and mean EPT relative abundance were highly correlated at all transects, with the exception of Asotin Slough (R = 0.40 with Asotin, R = 1.00 without Asotin). Here, EPT biomass was proportionally much higher than EPT abundance, owing to large numbers of smaller, larval macroinvertebrates recovered in the rock baskets during fall/winter. This site experiences a flow regime much different from the regimes of the others surveyed, characterized by swift currents proximal to the Hells Canyon Reach. North American ETP families are generally most represented (highest diversities) in cooler, lotic, and rocky-bottomed aquatic environments similar to Asotin Slough; however, they do exploit warmer, lentic environments with finer substrates, to varying degrees of success (Merritt and Cummins 1996). EPT biomass was highest at Asotin and generally decreased as Lower Granite Reservoir became more lentic. The same was true for EPT relative abundance, although this metric was highest at Clarkston (19.1%). Relative abundance of EPT genera at Snake River monitoring locations ranged from 0.0% to 19.1%, generally comparable to values reported in the literature for first- and second-order

4.25 Final Report streams in other locations (Figure 4.28). Relative abundances of EPT genera reported in previous studies conducted on first- and second-order streams in West Virginia, North Carolina, and New Zealand range from 1.0% to 12.5%, 1.32% to 5.28%, and 0.0% to 29.0% of sample, respectively (Figure 4.28; Appendix E; Merritt and Cummins 1996; Collier et al. 1998; Stone and Wallace 1998; Kaller and Hartman 2004; Hieber et al. 2005).

25% Lower GraniteLittle Lower Ice Harbor Other Studies of Goose Monumental 1st and 2nd Order Streams 20%

15%

10%

5% Overall Mean Relative ETP Abundance

0%

Transect

Figure 4.28. Overall mean ETP relative abundance per transect, including other studies of first and second-order streams. While these streams are of a lower order and have different morphological characteristics, overall mean ETP relative abundance is similar to what was found on the lower Snake River.

Sites within the Lower Granite impoundment harbored a significantly greater proportion and biomass of ETP than sites within the Little Goose impoundment. Elsewhere, mean EPT relative abundance exceeded 10% of the sample at Tucannon, Devil’s Bench, and Sheffler Shoal. Otherwise, neither metric fit any pattern upstream to downstream, and there were no significant differences between modified and unmodified sites, free-flowing, embayment, main-stem steep lateral bed slope, and main-stem gradual lateral bed slope areas, or sites where Chinook salmon were found versus sites where they were absent. EPT biomasses and relative abundances were virtually identical on alluviums and angular colluviums. Mean EPT biomass was not correlated to mean periphyton biomass but did have a slight correlation to phytoplankton density (R = 0.40). Asotin has both the highest mean EPT biomass and highest phytoplankton density. Also, there were significant seasonal differences: EPT biomass and relative abundance were much higher during the spring and summer than during the fall/winter (P < 0.05).

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4.4.2 Family Diversity Index

Mean family diversity, using Shannon’s index, ranged between 1.05 and 2.25 across sites during the study period. A diversity value less than 1 denotes a community that lacks an even distribution of abundance across taxa, whereas higher diversity values indicate greater evenness and community complexity (Edwards et al. 1974; Osborne et al. 1980). The values calculated with 2010–2011 data are comparable to previous studies on the Hanford Reach of the Columbia River and lower Snake River (Edwards et al. 1974; Stark 2001). Mean diversities were highest at Clarkston, Devil’s Bench, and Sheffler Shoal and generally increased throughout the year at all locations (Figures 4.29 and 4.30). Mean diversity varied seasonally, with summer samples being significantly more diverse than spring, and both seasons’ samples were significantly more diverse than fall/winter (P < 0.05; similar to biomass and relative abundance). However, there were no sites or site classifications with the distinction of significantly higher or lower mean diversity values. Mean diversity was not correlated to either mean periphyton biomass or mean phytoplankton density. Mean diversity of macroinvertebrates tended to be greater on angular colluviums (at 7 transects), although this difference was not significant when all 24 sample sites and 12 transects were compared (Figure 4.31).

Overall measures of biomass, relative abundance (both relative to EPT taxa), and diversity were highest at Clarkston, Devil’s Bench, and Sheffler Shoal. These metrics indicate that, in a comparative sense, conditions for aquatic macroinvertebrates are best at these locations. Both the upper and lower sample sites at Clarkston and Sheffler Shoal are characterized by a main-stem location with a gradual, lateral bed slope and have fairly similar mean diversities (no significant differences). Devil’s Bench, however, is divided between an embayment and main-stem location (upper) with a steep, lateral bed slope (lower), and diversity was higher in the embayment (P = 0.165). Collectively, these observations support the view that shallow-water areas have higher levels of secondary productivity.

2.0 Lower Granite Little Lower Ice Harbor 1.8 Goose Monumental

1.6

1.4

1.2

1.0

0.8

0.6

0.4 Mean Diversity (Shannon's Index) (Shannon's Diversity Mean 0.2

0.0

83% of Chinookfound here Transect

Figure 4.29. Mean macroinvertebrate diversity (Shannon’s index), by site.

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Fall / Winter Spring Summer 2.5

2.0

1.5

1.0

Mean Diversity (Shannon's Index) (Shannon's Diversity Mean 0.5

0.0 Asotin Slough Clarkston Knoxway Bench Knoxway Bay Offield Landing Transect

Fall / Winter Spring Summer 2.5 Little Lower Ice Harbor Goose Monumental 2.0

1.5

1.0

Mean Diversity (Shannon's Index) 0.5

0.0 Illia Dunes New York Tucannon Devil's Bench Burr Canyon Burr Shoal Sheffler Shoal Island River Transect

Figure 4.30. Mean seasonal diversity (Shannon’s index), by site, in Lower Granite, Little Goose, Lower Monumental, and Ice Harbor Reservoirs. Mean diversity was significantly greater during the summer than during the other seasons (P < 0.05).

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Alluviums Colluviums 2.0 Lower Granite Little Lower Ice Harbor 1.8 Goose Monumental 1.6 1.4 1.2 1.0 0.8 0.6 0.4 0.2

Mean Diversity (Shannon's Index) (Shannon's Diversity Mean 0.0

83% of Chinookfound here Transect

Figure 4.31. Overall mean macroinvertebrate diversity (Shannon’s index), by site, on alluvium versus colluvium. Although diversity was generally higher on angular colluvium substrate than alluvium substrate, the difference was not statistically significant.

4.4.3 DEPT Index

When compared with mean Chinook salmon CPUE (electrofishing) and n (seining), mean DEPT biomass per site does not appear limiting (Figure 4.32). The biomass of the orders Diptera, Ephemeroptera, Plecoptera, and Trichoptera (DEPT), similar to EPT, decrease from upstream to downstream through Lower Granite Reservoir (Figure 4.32). Sites within Little Goose Reservoir harbor significantly less DEPT biomass than other reservoirs in the study area. NPMR analysis reveals a strong, positive correlation between DEPT biomass and seining CPUE at sites upstream of rkm 120 where juvenile Chinook salmon were found (xR2 = 0.71; Figure 4.33). Mean gravimetric DEPT increased significantly from fall/winter to summer and from spring to summer, although differences in DEPT biomass between fall/winter and spring were not significant (P < 0.05; Figure 4.34). Similar seasonal differences were seen when comparing biomass between alluvium substrate and angular colluvium substrate, and although angular colluvium tended to host slightly greater gravimetric DEPT overall, this difference was not significant (P < 0.05; Figure 4.35). It should be noted that the sum of macroinvertebrate biomasses collected from alluviums and colluviums does not equate to the biomass of the composite sample, because the composite includes macroinvertebrates dislodged from the different rock types or taken from other surfaces on the basket, which can therefore not be differentiated. These samples, sieved from the buckets into which baskets were lowered to await sorting, often contained larger invertebrates, such as crayfish.

When spring gravimetric data were examined, there were significantly higher mean DEPT biomasses (although not mean DEPT relative abundances) on angular colluviums (P < 0.05; Figure 4.36). This may be a result of higher spring flows; the greater surface heterogeneity of angular colluviums, many of which included vacuous pockets, likely provided greater refugia from high flows than alluviums. Although mean DEPT biomass was not correlated with periphyton biomass, there was a slight relationship to mean

4.29 Final Report zooplankton density, with the greatest of both metrics found at Asotin Slough (R = 0.50). Mean DEPT relative abundance was similarly correlated to mean zooplankton density (R = 0.40).

Mean DEPT Biomass Chinook (CPUE) Fall Chinook Subyearlings 0.5 300.0 Lower Granite Little Lower Ice Harbor 0.4 Goose Monumental 250.0 0.4

0.3 200.0

0.3 150.0 0.2 Biomass (mg DM)

0.2 100.0 (CPUE,Chinook n)

0.1 50.0 0.1

0.0 0.0

Site

Figure 4.32. Mean DEPT biomass (mg DM), by transect, with Chinook salmon sampled via electrofishing (CPUE) and seining (n). There was no difference in DEPT biomass between locations where Chinook salmon were present versus absent however the biomass was significantly lower in Little Goose Reservoir.

Figure 4.33. NPMR projection graph depicting the relationship between seining CPUE of subyearling Chinook salmon (CH0seine), river kilometer (rkm), and biomass of DEPT macroinvertebrates (MIbiom). Figure is oriented to display the relationship between CPUE and DEPT biomass. Seining CPUE of subyearling Chinook salmon increases with increasing DEPT biomass at sites between rkm 100 and rkm 250.

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Fall / Winter Spring Summer 0.7 Lower Granite

0.6

0.5

0.4

0.3

0.2 Mean (mg DM) DEPT Biomass 0.1

0.0 Asotin Slough Clarkston Knoxway Bench Knoxway Bay Offield Landing

0.7 Little Goose Lower Monumental Ice Harbor 0.6

0.5

0.4

0.3 DEPT BiomassDM) (mg 0.2 Mean 0.1

0.0 Illia Dunes New York Tucannon Devil's Bench Burr Canyon Burr Shoal Sheffler Shoal Island River Transect

Figure 4.34. Mean seasonal DEPT biomass (mg DM), by site, in all reservoirs. Mean DEPT biomass increased significantly from fall/winter to summer and from spring to summer, although differences in DEPT biomass between fall/winter and spring were not significant.

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Alluviums Colluviums 0.20 Lower Granite Little Lower Ice Harbor 0.18 Goose Monumental 0.16 0.14 0.12 0.10 0.08 0.06

Mean Biomass (mg DM) 0.04 0.02 0.00

Transect 83% of Chinookfound here Figure 4.35. Overall mean DEPT biomass (mg DM), by site, for alluvium substrate and angular colluvium substrate.

Alluvium Colluvium 2.5 Lower Granite Little Lower Ice Harbor Goose Monumental 2.0

1.5

1.0

0.5

Mean Spring DEPT Biomass0.0 (mg DM)

Site 83% of Chinookfound here Figure 4.36. Mean spring macroinvertebrate DEPT biomass (mg), by site, on alluvium versus colluvium. Mean diversity was significantly higher on colluvium (P = 0.05).

Mean DEPT relative abundance was found to be significantly higher at Asotin Upper and Clarkston Upper than at Burr Shoal Lower (P < 0.05; Ice Harbor); all Ice Harbor sites had a significantly lower DEPT abundance compared to Lower Granite and Lower Monumental sites (P < 0.05; Figure 4.37). There was no correlation between mean DEPT relative abundance and Chinook salmon sampled via electrofishing (CPUE) or seining (Figure 4.38). Mean DEPT relative abundance was significantly greater along free-flowing reaches (i.e., at Asotin) than those sites in cove or embayment areas (P < 0.05; Figure 4.38).

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Seasonally, mean DEPT relative abundance peaked during spring and dropped during summer (not significant), perhaps aligning with the springtime phytoplankton bloom. Overall results for alluvium substrate and angular colluvium substrate were similar to other DEPT results. Alluvium substrate at the unmodified Knoxway Bench site (Upper) contained a significantly (P < 0.05) higher percentage of DEPT (44%) than did the modified site (Knoxway Bench Lower; 7%), perhaps due to the gravel riverbed composition of the unmodified site. Macroinvertebrates are thought to prefer fine and coarse gravel to sand and boulders (Bourassa and Morin 1995). Cummins and Lauf (1969) and Erman and Erman (1984) confirm that, in their experiments, abundance and taxa richness increased as substrate size increased on substrates ranging from 2 mm to 32 mm in diameter. Flecker and Allan (1984) also note macroinvertebrates’ preference of gravel, explaining that its surface heterogeneity and ample interstices may provide the most refugia for the insects.

Mean biomasses and relative abundances of DEPT genera within Lower Granite reservoir do not appear to be limiting the area’s ability to support Chinook salmon populations. There were not as many Chinook salmon found at Asotin, where the highest mean DEPT biomasses and relative abundances were measured. However, this result may simply indicate greater inaccessibility to this site for seining and other sampling personnel during high spring and early summer flows.

DTEP Relative Abundance Chinook (CPUE) Fall Subyearling (n) 60.0% 300.0 Lower Granite Little Lower Ice Harbor Goose Monumental 50.0% 250.0

40.0% 200.0

30.0% 150.0

20.0% 100.0 Chinook (CPUE, n) Mean DEPT Relative DEPT Mean Abundance 10.0% 50.0

0.0% 0.0

Site

Figure 4.37. Mean DEPT relative abundance (%), by site, with Chinook salmon sampled via electrofishing (CPUE) and seining (n). Mean DEPT relative abundance is significantly higher at Asotin Upper and Clarkston Upper than Burr Shoal Lower (P < 0.05). Ice Harbor sites have a significantly lower DEPT abundance than do Lower Granite and Lower Monumental sites (P < 0.05). DEPT relative abundance does not appear limiting to Chinook salmon.

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60%

50%

40%

30%

20% Relative Abundance 10%

0%

Free-flowing Site Embayment Figure 4.38. Mean DEPT relative abundance in free-flowing and embayment areas of Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs. Free-flowing reaches have a significantly higher mean DEPT relative abundance (P < 0.05).

4.5 Water Quality Monitoring

4.5.1 Water Temperature

Continuous hourly temperature data were collected at all sites from November 3, 2010, to November 22, 2011 (Appendix F, Table F.1 and Figures F.1–F.24). During early November 2010, temperatures were approximately 10°C and within a month dropped to less than 5°C for the duration of winter, until early March. The lowest daily mean temperature was 1.3°C at Clarkston Upper in February. From March through mid-July, there was a steady warming of temperatures from approximately 5°C to 20°C. During July, August, and September, temperatures frequently exceeded 20°C, similar to previous results on the lower Snake River (Cook et al. 2006, 2007; Seybold and Bennett 2010). The highest daily mean temperature was seen during August at Asotin Slough Upper (23.9°C) and the lowest during February at Clarkston Upper (1.3°C). Fall/winter (November–March) temperatures averaged approximately 5.5°C, while spring (April–June) temperatures averaged 10.8°C. Summer (July– November) temperatures were warmer with an average of 19°C (Figure 4.39). There were no significant differences at the 95% confidence interval between pools, types of sites, sites where Chinook salmon were present or absent, or transects (Appendix F, Figures F.25 and F.26).

Previous work has shown that juvenile Chinook salmon are negatively affected by temperatures that exceed 24°C (Brett 1952) or 25°C (Geist et al. 2010). This does not account for other environmental effects that may occur at higher temperatures, such as increased susceptibility to gas bubble disease (Ebel et al. 1971). Sullivan et al. (2000) designated temperature below 21°C as the zone of preference, 21°C–23.5°C as the zone of tolerance where there is a behavioral adjustment but no mortality, 23.5°C–26.5°C as the zone of resistance where mortality can occur in proportion to length of exposure,

4.34 Final Report and finally above 27°C as the upper critical lethal limit where there is rapid mortality for all juvenile salmonids. Temperatures on the Snake River were previously measured above 24°C within Lower Granite Reservoir during 2003 (Cook et al. 2006) and 1992 (Bennett et al. 1997b); however, during our 2011 study, daily mean temperatures remained below 24°C. Temperatures remained below 25°C during the summer of 2008 when they were measured throughout the lower Snake River for previous research (Seybold and Bennett 2010).

Figure 4.39. Hourly temperature separated by season.

Diel temperature variations were typically less than 1°C but were as high as 7°C at Clarkston Lower (Figure 4.40) and were most common during the summer months. The sites with the greatest diel fluctuation were Clarkston Upper and Lower, Offield Landing Upper and Lower, and New York Island Upper and Lower. Such fluctuation at New York Island could be attributed to a phenomenon in which strong winds are thought to “hold” the upper water column in place, causing increased heating. This phenomenon has been observed at mid-reservoir locations in the Lower Monumental and Little Goose impoundments (Cook et al. 2006), which include the New York Island site.

Depth stratification of temperature was quantified by looking at the difference between deep and shallow sensors, and how large that difference was during different times of the year. Temperature differences were minimal during the fall, winter, and spring (October–June) but became more pronounced during the summer (July–August; Figure 4.41 and Appendix F, Figures F.27–F.50). During the winter, there was less than 1°C variability between the deep and shallow sensors with the deeper sensors having a warmer temperature. The locations of shallow sensors were affected more by air temperature than were the deep sensors. Beginning in June, deep sensors were up to 7°C cooler than shallow sensors at

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Clarkston Lower. Stratification was most obvious at the Clarkston, Knoxway Bench, Knoxway Bay, Offield Landing, New York Island, and Devil’s Bench sites (Figure 4.42).

Clarkston Lower 23 22 21 20 19 18 17

Temperature16 (°C) 15 14 13 8/1 8/3 8/5 8/7 8/9 8/11 8/13 8/15 Date

Figure 4.40. Diel fluctuations at Clarkston Lower for a 2-week time period from August 1, 2011, to August 15, 2011.

Releases of cold water from Dworshak Reservoir in the summer to the Clearwater River contribute colder water to the Snake River at their confluence in Clarkston, with differences as high as 11°C observed during the summer (Cook et al. 2006). This influence was apparent with the cooler temperatures at our deep sensors at Clarkston, Knoxway Bench, Knoxway Bay, and Offield Landing. Once the cold water passed Lower Granite Dam, it became mixed and temperature gradation was no longer apparent at Illia Dunes. However, temperature gradation was observed downstream in Little Goose reservoir at New York Island. Similarly, the water was again mixed at Little Goose Dam with no apparent temperature gradation at the Tucannon River site, although temperature gradation was observed immediately upstream of Lower Monumental Dam at the Devil’s Bench site. Based on our temperature data, river water was well mixed downstream of Lower Monumental Dam at sites within Ice Harbor reservoir with little evidence of temperature gradation. This result is consistent with other temperature studies in the Snake River (Cook et al. 2006). Temperature gradation was most apparent during August and began to disappear during mid-September, consistent with expected mixing patterns of Dworshak Dam cold-water releases based on previous Snake River observations (Figure 4.41B; Cook et al. 2007).

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A) Offield Landing Lower Deep Shallow Mid 25

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Mean Daily Temperature (°C) Temperature Daily Mean 0 ND J FMAMJ J AS Date

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Figure 4.41. Temperature data from the deep, mid, and shallow sensors at Offield Landing Lower from November 2011 to October 2011 (A), and during the time period August 15, 2011 to September 22, 2011, showing the temperature variation between deep and shallow sensors (B).

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Figure 4.42. Boxplot showing the temperature difference between the deep and shallow sensors for each site. This plot is for the time period from August, 1, 2011 to September, 17, 2011, when depth stratification is most apparent.

4.5.2 Dissolved Oxygen

DO ranged from 85% to 115% throughout the year (Figure 4.43 and Appendix F, Table F.2) and values were similar to those previously reported on the lower Snake River (Seybold and Bennett 2010). Fall/winter (November–March) dissolved oxygen levels were approximately 95% and then increased to approximately 105% in the spring (April–June). DO dropped again during the summer (July–September) to 95%–100%. Spring DO levels were significantly higher at the 95% confidence interval than those in the fall or winter (Figure 4.43). DO levels are typically higher in the spring due to spill at the dams and increased levels of TDG. TDG values ranged up to 127% during the spring when DO was also elevated (Figure 4.5). We did not examine submerged macrophyte coverage during our study. However, previous work has shown that the Ice Harbor Reservoir also has the highest total submerged macrophyte biomasses and overall macrophyte coverage, which could contribute to higher DO levels (Seybold and Bennett 2010).

There were no significant differences across pools, types of sites, or sites where Chinook salmon were present or absent for DO (Appendix F, Figure F.51). There were few significant differences between sites for DO (Appendix F, Figure F.54). DO appeared slightly higher at downstream locations, with significant differences observed only between Sheffler Shoal Lower (higher DO) and Knoxway Bay Upper (lower DO; Appendix F, Figure F.54).

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Figure 4.43. Seasonal variability of dissolved oxygen with all sites combined.

Depth stratification of DO was measured during vertical water-quality profiles, with DO varying as much as 19% (Appendix F, Table F.3). DO levels were typically higher at the bottom of the water column and then decreased toward the surface. Due to the fact that we used a membrane DO sensor, this trend may be a remnant of the probe slowly equilibrating to DO levels during the profile. Occasionally, mid-profile increases in DO were observed, but usually the trend was fairly constant, whether increasing or decreasing.

Continuous hourly monitoring of DO was available from selected sites during spring monitoring (April 5–July 8). Sheffler Shoal Lower had the highest DO levels (115%) compared to approximately 100%–105% for Clarkston Lower and Knoxway Bench sites during the first monitoring period (April 5–April 29; Figure 4.44). There were significant diel fluctuations in the DO data (Figure 4.44), up to 6% at Sheffler Shoal Lower. Knoxway Bench Upper and Lower had the longest record of data and were quite similar for all water quality parameters. During initial spring monitoring (April 5–April 29), Knoxway Bench Upper had slightly higher DO levels, but this transitioned to lower DO values than were observed at Knoxway Bench Lower later in the monitoring period, during June (Figure 4.44).

Results from the cluster analysis indicated that water quality was generally similar among sites that were located in proximity to one another and divided the sites into three main groups (Figure 4.45). Group 1 had moderate DO levels relative to the other sites and consisted of sites near the mouth of the Clearwater River (Asotin and Clarkston). Group 2 had low DO levels and consisted of sites in the forebay of Lower Granite Dam (Knoxway Bench, Knoxway Bay, and Offield Landing) and three transects downstream of Lower Granite Dam (Illia Dunes Upper, New York Island Upper, and Devil’s Bench Lower). Group 3 had moderate to high DO levels and consisted of all sites downstream of Lower Monumental Dam (Burr Canyon, Burr Shoal, and Sheffler Shoal) and several upstream transects (Illia Dunes Lower, Tucannon River Upper and Lower, Devil’s Bench Upper, and New York Island Lower). DO was substantially higher at Illia Dunes lower compared to Illia Dunes upper (Figure 4.45).

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This may be attributed to the large number of submerged macrophytes present at Illia Dunes Lower, which may have increased respiration and consequently explain higher DO levels there. Conditions at Illia Dunes Lower, a shallow backwater area characterized by low water velocity, are highly favorable for macrophyte growth.

Clarkston Lower Knoxway Bench Upper Knoxway Bench Lower Sheffler Shoal Lower 120 115 110 105 100

LDO%Sat 95 90 85 80 4/4/11 4/24/11 5/14/11 6/3/11 6/23/11 Date

Figure 4.44. Dissolved oxygen long-term Minisonde data showing elevated levels at Sheffler Shoal Lower.

Figure 4.45. Cluster analysis results showing site groupings based on trends in water quality. Water quality variables including dissolved oxygen (DO), pH, and specific conductance were considered during the cluster analysis.

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4.5.3 pH

pH ranged from approximately 6.5 to 8.5 throughout the year (Figure 4.46 and Appendix F, Table F.2). Previously reported pH values have varied widely. During 2005, pH values varied between 7.6 and 9.3 while during 2006, they varied from 5.7 to 7.1 (Seybold et al. 2006), and during 2009, pH values varied between 8 and 10 measured at the same sites we monitored (Seybold and Bennett 2010). The total maximum daily load (TMDL) levels for the upper Snake River Hells Canyon area have been established by the U.S. Environmental Protection Agency (EPA) at 7 to 9. Data from our current study generally fall within this range, with the exception of pH values below 6.5 during the spring (New York Island Lower; Appendix F, Table F.2). Values of pH were not significantly different throughout the year but had much more variability during the spring (Figure 4.46). Tributary inputs may contribute to pH variability in the main-stem Snake River, particularly when runoff is at its peak during the spring.

Figure 4.46. Seasonal variability of pH with all sites combined.

There were no significant differences across pools, types of sites, or sites where Chinook salmon were present or absent for pH (Appendix F, Figure F.52). There were few significant differences between sites for pH (Appendix F, Figure F.55). pH values were less variable downriver and were typically slightly lower. The Asotin sites had significantly higher pH values than most in the Ice Harbor Reservoir (Appendix F, Figure F.55).

Depth stratification during vertical water quality profiles of 1.1 pH units was observed (Appendix F, Table F.3); however, typically pH values did not vary more than 0.3 pH units. pH was generally slightly more acidic on the bottom and became more basic as the probe was moved toward the surface.

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The cluster analysis characterized group 1 (Asotin and Clarkston) as having relatively high pH values compared with the other sites. Groups 2 and 3 were characterized by low to moderate pH. Despite the differences in pH between sites, pH is not limiting fish use of habitat at any of the locations that were monitored.

4.5.4 Specific Conductance

Specific conductance varied from 100 to 400 µS/cm over the year (Figure 4.47 and Appendix F, Table F.2). Specific conductance was significantly higher during the fall/winter (approximately 300 µS/cm) and then dropped to between 150 and 200 µS/cm during the spring and summer (Figure 4.47). Water from the Clearwater River has very low specific conductance (Arntzen et al. 2001). This influence, coupled with higher flow of the Clearwater and Snake rivers in the spring and summer, could contribute to lower specific conductance through the system. There were no significant differences across pools, types of sites, sites, or sites where Chinook salmon were present or absent for specific conductance (Appendix F, Figures F.53 and F.56). From the cluster analysis, sites with relatively high specific conductance were in Group 1 (Asotin and Clarkston). Both Groups 2 and 3 were characterized by low to moderate specific conductance.

Figure 4.47. Seasonal variability of specific conductance (µS/cm) with all sites combined.

4.6 Sediment Composition and Organic Content

The majority of the lower Snake River sediment is composed of material finer than 2 mm. Of this, there is more fine to very fine sand (0.25–0.063 mm) than medium to very coarse sand (0.25–2 mm; Figure 4.48 and Appendix G, Table G.1 and Figures G.1–G.24). Sites where more than 75% of the sample consisted of gravel-size sediment (>2 mm) included Asotin Lower, Knoxway Bench Upper, and

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Devil’s Bench Lower. Across the lower Snake River, organic carbon values averaged 2.9% (Figure 4.48) and ranged from 0.66% at Clarkston Lower during June to 8.7% at Knoxway Bench Upper during June (Appendix G, Table G.1 and Figures G.5–G.29).

All Sites Combined 60 50 40 30 20

Percent of Sample 10 0 Gravel Med. -V.C. F. - V.F. Silt and Percent Sand Sand Finer Organic Carbon Size Class

Figure 4.48. Percentage of sample (by weight) for all sites combined across the lower Snake River for four size classes: gravel (>2 mm), medium to very coarse sand (Med.–V.C. Sand; 0.25–2 mm), fine to very fine sand (F.–V.F. Sand; 0.063–0.25 mm), and silt and finer (<0.063 mm).

The Asotin site had the highest percentage of gravel, followed by the main-stem locations with a steep lateral bed slope; however, these differences were not significant. The gravel content of backwater and main-stem areas with gradual lateral bed slopes did not differ from one another, but both of those site types had significantly less gravel than Asotin and areas with a steep lateral bed slope (Figure 4.49 and Appendix G, Figure G.25). There were no significant differences between the types of sites for the medium to very coarse sand fraction (Appendix G, Figure G.26). Asotin and main-stem locations with a steep lateral bed slope (Knoxway Bench Upper, Offield Landing Upper and Lower, Tucannon River Lower, and Devil’s Bench Lower) were similar, with very low percentages of fine to very fine sand. Main-stem locations with a gradual lateral bed slope (Clarkston Upper and Lower, Knoxway Bench Lower, Illia Dunes Upper, New York Island Upper and Lower, Burr Canyon Upper and Lower, Burr Shoal Lower, and Sheffler Shoal Upper and Lower) had increased percentages of fine to very fine sand, with the greatest amounts in backwater areas (Knoxway Bay Upper and Lower, Illia Dunes Lower, Tucannon River Upper, Devil’s Bench Upper, and Burr Shoal Upper; Figure 4.49 and Appendix G, Figure G.27). Sites in Little Goose reservoir had significantly less silt than Lower Monumental and Ice Harbor sites, and Asotin had significantly less silt than all other types of sites (Appendix G, Figure G.28).

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Figure 4.49. Gravel (>2 mm) and fine to very fine sand (0.25 to 0.62 mm) for the various site types. Notches within box plots represent the uncertainty about the medians. Overlapped notches indicate that the medians of the two groups differ at the 95% confidence level. The center of the notched plot is the median and the upper and lower bounds are the 25th and 75th percentiles.

Similar to previous results on the lower Snake River (Seybold and Bennett 2010), we found no correlation between organic content and the percentage of sample less than 2 mm (R2= -0.2807; P = 0.9725). However, there was a correlation between organic content and both the silt and finer fraction and the medium to very coarse sand fraction. Percentage organic matter was negatively correlated (R2= –0.43; P = 0.301) with the medium to very coarse sand fraction of the sample and positively correlated (R2 = 0.52; P = 0.0943) with the silt and finer fraction, but neither of these associations was statistically significant (α = 0.05). Asotin had significantly less organic content than all other sites (Figure 4.50). Main-stem locations with gradual lateral bed slope had significantly less organic content than main-stem locations with steep lateral bed slope (Figure 4.50). There was no significant difference in organic content between sites where Chinook salmon were present and absent (Figure 4.50).

We evaluated one location that was previously modified to create additional shallow rearing habitat for salmonids (Knoxway Bench Lower). The sediment composition at this location differed from the adjacent, unmodified location (Knoxway Bench Upper). Gravel dominated Knoxway Bench Upper (78% of the sample) where there was also a higher percentage of organic content (6.8%), compared to 2% for Knoxway Bench Lower. Knoxway Bench Lower consisted of 65% medium to very coarse sand (0.25–2 mm) and 26% fine to very fine sand (0.063–0.25 mm).

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Figure 4.50. Notched box plots showing the percentage organic carbon across types of sites, pools, and sites where Chinook salmon were present or absent.

Very few studies have examined organic matter contents in relation to salmon rearing locations or food sources. One study, in a North Carolina estuary, showed that areas with greater biomass and species richness of benthic macroinvertebrates were associated with higher salinity and lower organic matter (<6% organic content) in sandy sediments (Chester et al. 1983). Organic content in our study ranged from 0.66% to 8.7%, seasonally, but when averaged across the entire year, only Knoxway Bench Upper (6.7%) was greater than 6% organic material. Therefore, according to the Chester et al. (1983) study, the majority of our sites are not limiting in organic content and should have sufficient biomass and species richness. The three transects that had season averages above 6% organic content were Knoxway Bench Upper in June (8.7%), Knoxway Bay Upper in April (6.6%), and Offield Landing Lower in June (6.4%).

Throughout the lower portion of our study area, we expected little seasonal variability in sediment grain-size distribution. Our ability to quantify such variability was somewhat influenced by the sampling technique used to collect sediments (i.e., a Ponar dredge is less effective for gravel-size sediment). However, some seasonal variability was noted at the Clarkston Upper location, where our temperature anchor line was buried under approximately 1–2 ft of sediment during high river discharge during the spring. Underwater video surveys could be used in conjunction with a Ponar dredge to characterize the grain-size distribution in locations where large gravel is present (Groves and Chandler 1999; Mueller 2005; Geist et al. 2006; Hanrahan et al. 2007).

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Sediment sampling indicated that sites where Chinook salmon were present had significantly more medium to very coarse sand and less silt than sites where Chinook salmon were absent (Figure 4.51 and Appendix G, Figures G.25 and G.27).

Figure 4.51. Notched box plots of the medium to very coarse sand fraction (0.25 to 2 mm) and silt and finer fraction (<0.062 mm) for locations where Chinook salmon were present and absent.

Results from NPMR analysis indicated that the distribution of Chinook salmon among the sites was influenced most strongly by geographic location and the percentage of gravel collected in dredge samples. Within areas where Chinook salmon were most commonly found, electrofishing CPUE was generally negatively correlated with the percentage of gravel collected in dredge samples (Figures 4.11 and 4.52; xR2= 0.71 and xR2 = 0.49). Although the other substrate classes (silt and finer, fine to very fine sand, and medium to very coarse sand) explained less of the variability in seining CPUE of subyearling fall Chinook salmon and were not included in the “best” model, some relationships were observed. Between rkm 120 and 230, where most subyearling fall Chinook were sampled, CPUE was positively correlated with the percentage of fine to very fine sand (Figure 4.53; xR2 = 0.47) and the percentage of medium to very coarse sand (Figure 4.54; xR2 = 0.52) and negatively correlated with the percentage of silt (Figure 4.55; xR2 = 0.45) in dredge samples. Using NPMR, we tried to examine predator preferences in relation to sediment size but found no relationships. Predators were present in the entire reservoir system and were found in all types of habitats.

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Figure 4.52. NPMR projection graph depicting the relationship between electrofishing CPUE of juvenile Chinook salmon (CHefish), river kilometer (rkm), and percentage gravel in dredge samples (Gravel). Figure is oriented to display the relationship between CPUE and percentage gravel. Dams are located at rkm 15.6 (IHR), rkm 66.9 (LMN), rkm 113.1 (LGS), and rkm 172.7 (LGR). Electrofishing CPUE is highest at low gravel percentages within locations upstream of rkm 120.

Figure 4.53. NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon (CH0seine), river kilometer (rkm), and percentage of fine to very fine sand in dredge samples (SmSand). Dams are located at rkm 15.6 (IHR), rkm 66.9 (LMN), rkm 113.1 (LGS), and rkm 172.7 (LGR).

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Figure 4.54. NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon (CH0seine), river kilometer (rkm), and percentage of medium to very coarse sand in dredge samples (LgSand). Dams are located at rkm 15.6 (IHR), rkm 66.9 (LMN), rkm 113.1 (LGS), and rkm 172.7 (LGR).

Figure 4.55. NPMR projection graph depicting the relationship between seining CPUE of subyearling fall Chinook salmon (CH0seine), river kilometer (rkm), and percentage of silt and finer sediments in dredge samples (Silt). Dams are located at rkm 15.6 (IHR), rkm 66.9 (LMN), rkm 113.1 (LGS), and rkm 172.7 (LGR).

During seining, qualitative estimates of the grain size were made to see if there was any relationship between the grain size of predominant substrate types and the number of juvenile Chinook salmon. Our sites were approximately 600 m long, with some significant variations in grain size throughout. Juvenile

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Chinook salmon were found more often over sand/silt (23 Chinook salmon/haul) compared with gravel (14 Chinook salmon/haul) when examined at the site measurement scale (Figure 4.56).

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Figure 4.56. The number of juvenile Chinook salmon found over each predominant sediment type when normalized by the number of seine hauls conducted at each type of site. Juvenile Chinook salmon were found more often over sand/silt substrate than gravel.

Using all three methods of analysis (quantitative grain-size data compared to electrofishing and seining results using notched boxplots; quantitative grain-size data compared to seining and electrofishing results using NPMR; qualitative grain-size data compared to seined fish at very specific seining areas), we found similar patterns of Chinook salmon presence.

Overall, juvenile Chinook salmon preferred areas with abundant sand and showed a negative association with gravel- and silt-sized classes of substrate. Previous research has shown that rearing salmon typically prefer larger substrates (>2 mm; Gibson 1993), and some studies have shown that growth and survival of juvenile salmonids can be negatively impacted with increasing amounts of fine sediments (Crouse et al. 1981; Suttle et al. 2004). However, preferred salmon rearing habitat is dependent on the system and many other factors, such as depth, velocity, light, and cover (Gibson 1993). Previous research on the Snake River has shown that juvenile Chinook salmon are found primarily over sand substrates (Bennett et al. 1988b–1998; Curet 1993; Connor et al. 2001; Keefer and Peery 2008). The Snake River is dominated by sand, and this may be why most Chinook salmon are found in sandy areas. It may also be true that velocity is a more important indicator for Chinook rearing location; Chinook are found mostly in low-velocity areas that also tend to have sand in the Snake River. Chinook food items such as zooplankton, larval fish, and chironomids are typically more abundant in low-velocity areas, causing Chinook to be found in sandy areas (Curet et al. 1993; USACE 2002).

Results from cluster analysis conducted to group sites with regard to substrate composition indicated that bed slope and hydraulic characteristics influenced substrate type. The free-flowing site (Asotin) and transects with steep bed slopes (Knoxway Bench Upper and Offield Landing Upper and Lower) were

4.49 Final Report grouped with Burr Canyon Lower, New York Island Upper, and Burr Shoal Lower and characterized as having moderate to high proportions of gravel, low to moderate proportions of coarse to very coarse sand, low to moderate proportions of fine to very fine sand, and low to moderate proportions of silt and finer sediments. Most transects located in backwater areas and at the mouths of tributaries, and those with gradual bed slopes, were grouped into one of two groups. Both groups were characterized as having low proportions of gravel but varied in their proportions of smaller sediments. Clarkston Upper and Lower, Knoxway Bay Lower, Illia Dunes Upper, Burr Shoal Upper, and Knoxway Bench Lower had moderate to high proportions of coarse to very coarse sand, low to moderate proportions of fine to very fine sand, and low proportions of silt. The other sites, which consisted of Knoxway Bay Upper, Tucannon River Upper and Lower, Devil’s Bench Upper, Sheffler Shoal Upper and Lower, Illia Dunes Lower, and New York Island Lower, were grouped due to their low proportion of medium to very coarse sand, moderate to high levels of fine to very fine sand, and moderate to high proportions of silt. Burr Canyon Upper was placed in its own group due to the moderate proportion of gravel and high proportion of silt obtained in dredge samples.

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5.0 Management Implications

Our overall findings indicate that the least potential adverse impact to biota during sediment management actions, including dredging operations, on the lower Snake River would occur during the winter, when the abundance of fishes and other aquatic organisms in shallow areas was lowest. Shallow- water areas with a gradual lateral bed slope were most productive in terms of the diversity and biomass of salmonid prey items, especially at locations upstream of New York Island. Lower Granite sites fitting this description (with the exception of Knoxway Bench Upper and Offield Landing) harbored the most juvenile Chinook salmon and macroinvertbrate prey items of all sites examined in the lower Snake River. Water depth at these locations was typically less than 5 m, contrasting with depths greater than 5 m found in 90% of Lower Granite Reservoir (Seybold and Bennett 2010). If suitable locations for the creation of additional shallow-water habitat within the deep portions of the Lower Granite impoundment can be identified, we would expect an increase in salmonid rearing habitat.

Specific study findings and their implications to sediment management activities are summarized in the following list. • Fish community distributions were similar to those previously observed in 2009, despite substantially higher river discharge during the current study year (2011). Suckers and non-predaceous minnows were the most abundant resident fish. The consistency of fish community distributions across study years evaluated suggests that fish communities in the lower Snake River are reasonably stable, despite annual hydraulic variability that occurs. • Approximately 83% of all juvenile Chinook salmon were found in the Lower Granite Reservoir and tailrace (upstream of rkm 120). Most of these sites, with the exception of Offield Landing and Knoxway Bench Upper, have a gradual lateral bed slope. This finding suggests that newly created shallow-water habitat would be most productive if created upstream of rkm 120 and characterized by a gradual lateral bed slope. • In general, juvenile Chinook salmon were found to prefer areas of sand (0.063–2 mm) that were characterized by little to no gravel (>2 mm) and very little silt (<0.063 mm). More ocean-type fall Chinook salmon subyearlings were found at Knoxway Bench Lower (modified site; gradual lateral bed slope) than Knoxway Bench Upper (unmodified site; steep lateral bed slope). Knoxway Bench Upper (unmodified) was dominated by gravel (78% of sample), while Knoxway Bench Lower (modified) consisted of 91% sand. At locations above rkm 120, sediment distribution of sand and the extent of DEPT biomass were positively correlated with CPUE of subyearling Chinook salmon during their early rearing and migration period. Thus, newly created shallow-water habitat should be dominated by sand to be most suitable for juvenile Chinook salmon. • No relationship was found between predator locations and the underlying sediment. Predators were found throughout the lower Snake River; smallmouth bass were the most frequently captured predator, followed by northern pikeminnow. We found no evidence that the creation of additional shallow-water habitat would create additional habitat for salmonid predators. However, we did not evaluate spawning traits of predator species. Previous research suggests that the creation of shallow- water habitat would benefit juvenile predator species as well as juvenile Chinook salmon (Schlosser 1987; Bryan and Scarnecchia 1992; Gadomski et al. 2001). Stomach content analysis of smallmouth bass showed that their diet consisted of less than 6% Chinook salmon by weight. Smallmouth bass diet was dominated by signal crayfish and non-salmonid fish species.

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• A new sampling device was developed to search for juvenile lamprey in deepwater habitat. No lampreys were observed within any of the 24 study sites evaluated during comprehensive surveys conducted during July and September. Searches for juvenile lamprey were conducted only in order to determine presence/absence within study sites selected based on attributes for salmonid rearing. Thus, there are likely many additional locations within the lower Snake River that have a large amount of suitable rearing habitat for Pacific lamprey. To delineate suitable spawning and rearing habitats, a comprehensive substrate survey of the lower Snake River would be needed. • Wintertime sediment management activities would not likely impact zooplankton and phytoplankton, which have highest densities later during the summer, further strengthening the notion that dredging should occur during winter months. • Daphnia were absent at locations with the greatest Chinook salmon abundance. This observation may indicate substantial planktivory at these locations. If this observation can be verified, Daphnia biomass might be increased via creation of additional shallow-water habitat. Daphnia numbers were highest in areas characterized by relatively small quantities of silt (e.g., Ice Harbor Reservoir), suggesting that silt should be minimized in the creation of new shallow-water habitat. • Relatively high EPT (Ephemeroptera, Plecoptera, and Trichoptera) macroinvertebrate family diversity and biomass at Clarkston, Devil’s Bench, and Sheffler Shoal indicate relatively high productivity of macroinvertebrates in these locations. These sites are characterized by a shallow lateral bed slope, a characteristic that should be considered in creation of new shallow-water habitat. Overall, the mean relative abundance of DEPT macroinvertebrates important in the diet of Chinook salmon (Diptera, Ephemeroptera, Plecoptera, and Trichoptera) was higher at Lower Monumental and Lower Granite sites than at Ice Harbor sites (with the greatest relative abundance at the lone free-flowing reach studied near Asotin). There was a strong, positive correlation of DEPT biomass with all sites upstream of rkm 120, roughly upstream of New York Island. This finding further strengthens the notion that sediment management actions creating additional salmonid rearing habitat in the vicinity of Lower Granite Reservoir would support adequate food sources for juvenile Chinook salmon. • Organic content of Snake River sediments exceeded 6%—and potentially limited the biomass and species richness of benthic macroinvertebrates—during the spring at Knoxway Bench Upper (8.7%), Knoxway Bay Upper (6.6%), and Offield Landing Lower (6.4%). The organic content of newly created shallow-water habitat should be monitored to avoid potential limitations on macroinvertebrate productivity that could occur. • During spring when Chinook salmon were present, DEPT biomass was greater on angular colluvium substrate than on alluvium substrate. Thus, locations with increased quantities of angular substrates having a high surface heterogeneity may yield greater DEPT biomasses. Although the bed of the lower Snake River is dominated by sand, shoreline areas characterized by angular colluvia may provide beneficial characteristics for salmonid food production. • During springtime, pH dropped below 6.5 within the tailrace of Little Goose Dam, and dissolved oxygen became supersaturated, especially at downstream locations, during spring spill operations. In general, however, the differences we measured between temperature, DO, and pH at the various study sites were not large enough to impact the relative rearing habitat quality for juvenile salmonids, including primary production as it relates to their food sources. It should be noted that our study was conducted during a high water year, and summertime temperatures were relatively low compared to those expected under lower discharge conditions. Increased temperatures during a lower water year have the potential to impact the habitat quality for rearing juvenile salmonids at these locations.

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6.0 References

Angradi TR. 1999. Fine sediment and macroinvertebrate assemblages in Appalachian headwater streams: A field experiment with applications for biomonitoring. Journal of the North American Benthological Society 18:48–65.

Arntzen EV, DR Geist, and TP Hanrahan. 2001. Substrate Quality of Fall Chinook Salmon Spawning Habitat, Hells Canyon Reach, Snake River, Idaho. PNWD-3114, Battelle–Pacific Northwest Division, Richland, Washington.

Arruda JA, GR Marzolf, and RT Faulk. 1983. The role of suspended sediments in the nutrition of zooplankton in turbid reservoirs. Ecology 64(5):1225–1235.

Barbour MT, J Gerritsen, BD Snyder, and JB Stribling. 1999. Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates and Fish. 2nd edition. EPA 841-B-99-002, Office of Water, U.S. Environmental Protection Agency, Washington, D.C.

Becker CD. 1970. Feeding bionomics of juvenile Chinook salmon in the central Columbia River. Northwest Science 44(2):75–81.

Becker CD. 1971. Food and Feeding of Juvenile Chinook Salmon in the central Columbia River in Relation to Thermal Discharges and Other Environmental Features. Submitted to Battelle–Northwest, Richland, Washington.

Benke AC, AD Hurynm, LA Smock, and JB Wallace. 1999. Length-mass relationships for freshwater macroinvertebrates in North America with particular reference to the southeastern United States. Journal of the North American Benthological Society 18(3):308–343.

Bennet DH and FC Shrier. 1986. Effects of Sediment Dredging and In-Water Disposal on Fishes in Lower Granite Reservoir, ID-WA. U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington.

Bennett DH, LK Dunsmoor, and JA Chandler. 1988a. Fish and Benthic Community Abundance at Proposed In-Water Disposal Sites, Lower Granite Reservoir. U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington.

Bennett DH, LK Dunsmoor, JA Chandler, and T Barila. 1988b. Use of Dredged Materials To Enhance Fish Habitat in Lower Granite Reservoir, Idaho-Washington. U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington.

Bennet DH, LK Dunsmoor, and JA Chandler. 1990. Lower Granite Reservoir In-Water Disposal Test: Results of the Fishery, Benthic, and Habitat Monitoring Program – Year 1 (1988). U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington.

Bennett DH, JA Chandler, and G Chandler. 1991. Lower Granite Reservoir In-Water Disposal Test: Results of the Fishery, Benthic and Habitat Monitoring Program – Year 2 (1989). U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington.

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Appendix A – Study Site Locations

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Appendix B – Study Conditions

(.xls file on CD)

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Appendix C – Fish Species

(.xls file on CD)

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Appendix D – Zooplankton, Phytoplankton, and Periphyton

(.xls file on CD)

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Appendix E – Macroinvertebrates

(.xls file on CD)

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Appendix F – Water Quality

(.xls file on CD)

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Appendix G – Sediment Composition

(.xls file on CD)