In 2006, the Portland District of the U.S. Army Corps of Engineers (USACE) contracted with the Pacific Northwest National Laboratory (PNNL) to conduct three studies using acoustic telemetry to estimate detection probabilities and survival of juvenile Chinook salmon at three hydropower projects on the lower Columbia River. The primary goals were to estimate detection and survival probabilities based on sampling with Juvenile Salmon Acoustic Telemetry System (JSATS) equipment, assess the feasibility of using JSATS for survival studies, and estimate sample sizes needed to obtain a desired level of precision in future studies. Tagging We conducted acoustic-telemetry survival studies on yearling and sub-yearling Chinook salmon at John Day Dam (JDA), The Dalles Dam (TDA), and Bonneville Dam (BON). We surgically implanted 2,501 yearling Chinook salmon in spring and 2,502 sub-yearling Chinook salmon in summer with passive integrated transponder (PIT) and JSATS acoustic tags. Fish were collected and tagged at the John Day Dam Smolt Monitoring Facility (SMF), and unintentional tagging mortality averaged 0.6% in spring and 0.7% in summer. Tagging seasons encompassed the peaks of the spring and summer runs of juvenile Chinook salmon. The spring tagging season was from May 13 to June 6, 2006, and targeted the yearling Chinook run, which peaked between May 20 and June 1, 2006. A 95-mm minimum length limitation on tagging did not restrict the lengths of fish that could be tagged in the spring, and the length frequencies of tagged and untagged yearling Chinook salmon in the juvenile bypass system (JBS) samples were very similar. The summer tagging season was from June 11 to July 13, 2006, and targeted the subyearling Chinook run, which peaked around July 1. The 95-mm minimum tagging length effectively eliminated about 23% of the run-of-river sub-yearlings from the sample because they were too small to tag without increasing tagging mortality. Tagging must include 80 to 100 mm subyearlings to be fully representative of the runof-river population at JDA in summer. All fish tagged in this study and released at or below JDA were implanted with JSATS tags that transmitted a coded signal transmitting once every 5 seconds (5 s tags) that were expected to last about 30 days, and fish that were released into the Snake River by other studies were implanted with tags that transmitted once every 10 s. We conducted a tag-life study using 100 10 s tags and 100 5 s tags randomly sampled from lots allocated to survival studies. The tag-life study verified that most tags lasted about as long as expected. All 10-s tags sampled from lots of tags implanted in Snake River fish lasted at least 57 days relative to an expected 55 days, and all the 5-s tags exceeded the expected 30-day life by about 5 days. No tag-life correction was needed or used for the 2006 survival studies in spring or summer because over 99% of tagged fish exited the study area before tags expired. Tag life and survivorship curves are presented in Appendix A.

This report should be cited as follows:Weiland, MA, GR Ploskey, JS Hughes, Z Deng, T Fu, J Kim, GE Johnson, GW Batten, ES Fischer, F Khan, SA Zimmerman, DM Faber, KM Carter, JW Boyd, RL Townsend, JR Skalski, TJ Monter, AW Cushing, MM Meyer. 2011. Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival Proportions at John Day Dam, 2009. PNNL-20766. Draft report submitted by the Pacific Northwest National Laboratory to the U.S. Army Corps of Engineers, Portland District, Portland, Oregon.iii PrefaceThe study reported herein was funded as part of the Anadromous Fish Evaluation Program, which is managed by the U.S. Army Corps of Engineers (USACE). The Anadromous Fish Evaluation Program study code is SPE-P-08-03: Studies of Surface Spill at John Day Dam. The study was led by the Pacific Northwest National Laboratory (PNNL) for the USACE Portland District. The USACE technical leads were Robert Wertheimer, Sean Tackley, and Brad Eppard. The PNNL study project manager was Mark Weiland (509 427-5923). The data are archived at PNNL offices in North Bonneville, Washington.v Executive SummaryImproving the survival rate of juvenile salmonids migrating downstream through the Federal Columbia River Power System (FCRPS) continues to be a high priority for the USACE and the region. Many of these fish are from populations listed as threatened or endangered under the Endangered Species Act. Increasing survival rates is necessary to ensure sustainable salmon populations in the future and meet performance standards set forth in the 2008 Biological Opinion (BiOp) and 2008 Columbia Basin Fish Accords on operation of the FCRPS. The BiOp mandates that a 96% and 93% survival rate be achieved for spring and summer downstream migrating juvenile salmonids, respectively. At John Day Dam (JDA), the Portland District is evaluating the provision of surface-flow outlets (SFOs) as a means to increase fish-passage efficiency and in turn increase the fish-passage survival rate by reducing turbine passage of juvenile salmonids. The goal of the study reported here was to provide fish-passage and survival data necessary to evaluate the performance of the prototype SFO, called a top-spill weir (TSW), and the dam as a whole relative to the performance standards in the BiOp. The Portland District and regional fisheries managers will use the data to adaptively manage the configuration and operation of JDA to maximize the survival rate for juvenile salmonids. This is the report of research for the acoustic telemetry evaluation of juvenile salmonids during 2009 at JDA. The study was conducted by the Pacific Northwest National Laboratory and the University of Washington for the U.S. Army Corps of Engineers (USACE) Portland District. S.1 ObjectivesThe overall purpose of the acoustic-telemetry study at JDA during 2009 was to determine the best configuration and operation for JDA prior to conducting BiOp performance standard tests. The primary objective was to determine the best operation between 30% and 40% spill treatments. Route-specific, J...

Executive SummaryImproving survival rates of juvenile salmonids through the Federal Columbia River Power System (FCRPS) continues to be a high priority for the U.S. Army Corps of Engineers, Portland District. Many of these fish are from populations listed as threatened or endangered under the Endangered Species Act of 1973. Increased survival rates are necessary to meet performance standards set forth in the 2008 Biological Opinion (BiOp) on FCRPS operations. The BiOp mandates 96% and 93% survival rates be achieved for spring and summer downstream migrating juvenile salmonids, respectively. At John Day Dam, the Portland District is evaluating the provision of surface flow outlets (SFOs) as a means to increase fish-passage efficiency and in turn increase passage survival rates by reducing turbine passage of juvenile salmonids. The goal of the study reported herein is to provide the passage and survival data necessary to evaluate the performance of the prototype SFO and the dam as a whole relative to the standards in the BiOp. The study was conducted by the Pacific Northwest National Laboratory and the University of Washington. The Portland District and regional fisheries managers will use the data to adaptively manage the configuration and operation of John Day Dam to maximize the survival rates of juvenile salmonids. ObjectivesIn this report, we present survival estimates, passage efficiencies, and fish behavior data for acoustictagged steelhead (STH), yearling Chinook salmon (YC), and subyearling Chinook salmon (SYC) passing through John Day Dam during 2008. We examined the data relative to two spill treatments, 30% versus 40% spill out of total water discharge through the dam, to assess the performance of SFOs, called topspill weirs (TSWs). The field study period was from April 29 to August 20, 2008. The objectives were as follows:• Survival Rates -Estimate single-and paired-release, route-specific, dam-passage, and concrete-passage survival rates for YC, STH, and SYC passing through John Day Dam for each of two spillway operational treatments.• Fish Passage -Estimate passage proportions among major passage routes, and calculate efficiency and effectiveness metrics for each of two spillway operational treatments for YC, STH, and SYC separately.-Estimate travel times (forebay residence and tailrace egress) of YC, STH, and SYC for each of two spill treatments.• Fish Behavior -Characterize fish behaviors, including forebay approach paths, for YC, STH, and SYC and compare approach paths with the final route of passage for each of two spill treatments.-Describe vertical and horizontal distributions and residence times of YC, STH, and SYC within the dam forebay. MethodsThis study used the Juvenile Salmon Acoustic Telemetry System (JSATS). We surgically implanted acoustic tags and passive integrated transponder tags in 3447 YC and 3450 STH in spring and in 5931 SYC in summer. Median lengths of tagged fish were as follows: YC = 158 mm; STH = 217 mm; SYC = 117 mm.Tagged YC and STH were released daily over a 29-day spr...

Executive SummaryIn 2007, the Portland District of the U.S. Army Corps of Engineers contracted with the Pacific Northwest National Laboratory (PNNL) to conduct an acoustic telemetry study to estimate the survival of juvenile Chinook salmon passing the spillway at Bonneville Dam. Fish longer than 95 mm were surgically implanted with Juvenile Acoustic Telemetry System (JSATS) and passive integrated transponder (PIT) tags, held overnight in tanks supplied with continuous flow of river water to allow time for recovery from surgery, and released between 1400 and 1700 hours on 16 days in spring and 14 days in summer. Some fish were released in the spillway forebay above the dam to create treatment-release groups that would pass through the spillway, and other fish were released 2 km downstream of the spillway in the tailrace to create reference-release groups that did not pass through the spillway. Reference releases in the tailrace began about 1 hour after the start of treatment releases in the forebay so that both groups would mix and pass through the common downstream tailwater about the same time of day. The common tailwater for our survival estimates was from the tailrace-release site 2 km downstream of the dam to the first or second of three tag-detection arrays located downstream of the dam. An array is a group of autonomous underwater receivers (nodes) deployed to listen for acoustic tags passing through an entire cross section of the river. Treatment fish were exposed to passage through < 76 m of spillway forebay, spill bays, and 2 km of tailrace that the reference-release groups avoided. Single-release estimates included survival from the point of release to the primary detection array or from the primary array to the secondary array and included losses of fish in the common tailwater. Paired-release survival estimates for spillway-passed fish to the tailrace-release site were calculated as the ratio of the survivals of treatment-release groups to the survivals of paired reference-release groups to remove effects of losses of fish in the common tailwater. The PNNL team released treatment fish in the forebay and a National Oceanic and Atmospheric Administration Fisheries team released reference fish in the tailrace. Some treatment fish were detected by spillway hydrophones and assigned a bay of passage based upon the location of the last of at least four detections of implanted acoustic tags. Detections of PIT tags in the Powerhouse 2 (B2) Corner Collector (B2CC) and B2 Juvenile Bypass System (B2 JBS) were used to assign non-spillway routes of passage. Major FindingsWe only tagged fish longer than 95 mm to avoid overburdening small fish and inducing unnecessary tag effects. This 95-mm minimum length for tagging did not restrict the lengths of fish that could be tagged in spring because the length of almost all yearlings exceeded 95 mm, and the frequencies of tagged and untagged yearling Chinook salmon in the JBS samples being of similar length were very similar. In contrast, the 95-mm minimum length to be el...

The USACE technical leads were Mr. Brad Eppard and Mr. Fred Higginbotham. The study was designed to evaluate the passage and survival of yearling and subyearling Chinook salmon and juvenile steelhead at McNary Dam as stipulated by the 2008 Biological Opinion and Fish Accords and to assess performance measures including routespecific fish passage proportions, travel times, and survival based upon a virtual/paired-release model. This study supports the USACE's continual effort to improve conditions for juvenile anadromous fish passing through Columbia River dams.