PNNL-22266 Prepared for the U.S. Army Corps of Engineers, Portland District, under an Interagency Agreement with the U.S. Department of Energy Contract DE-AC05-76RL01830 Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival at John Day Dam, 2011 FINAL REPORT Pacific Northwest National Laboratory University of Washington Pacific States Marine Fisheries Commission June 2013 DISCLAIMER This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor Battelle Memorial Institute, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. 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(9/2003) PNNL-22266 Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival at John Day Dam, 2011 FINAL REPORT MA Weiland SA Zimmerman TJ Carlson AL Miracle CM Woodley GR Ploskey SM Carpenter1 TD Mitchell1 JS Hughes Z Deng AW Cushing1 K Prather1 J Kim T Fu T Elder1 B Rayamajhi MJ Hennen1 JR Skalski2 DJ Etherington1 IM Royer1 ES Fischer RL Townsend2 MJ Greiner JP Duncan AG Seaburg2 F Khan KA Wagner GW Batten1 JJ Martinez June 2013 Prepared for U.S. Army Corps of Engineers, Portland District under an Interagency Agreement with the U.S. Department of Energy Contract DE-AC05-76RL01830 Pacific Northwest National Laboratory Richland, Washington 99352 1 Pacific State Marine Fisheries Commission, Portland, Oregon. 2 Columbia Basin Research, University of Washington, Seattle, Washington. This report should be cited as follows: Weiland, MA, CM Woodley, JS Hughes, J Kim, MJ Hennen, ES Fischer, JP Duncan, KA Wagner, SA Zimmerman, GR Ploskey, Z Deng, T Fu, JR Skalski, RL Townsend, AG Seaburg, GW Batten III, TJ Carlson, SM Carpenter, AW Cushing, T Elder, DJ Etherington, MJ Greiner, F Khan, JJ Martinez, AL Miracle, TD Mitchell, K Prather, B Rayamajhi, and IM Royer. 2013. Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival at John Day Dam, 2011. PNNL-22266. Final report submitted to the U.S. Army Corps of Engineers, Portland District, Portland, Oregon, by the Pacific Northwest National Laboratory, Richland, Washington. Preface This study was conducted by the Pacific Northwest National Laboratory (PNNL), the University of Washington (UW), and Pacific States Marine Fisheries Commission (PSMFC) for the U.S. Army Corps of Engineers (USACE), Portland District (CENWP). The CENWP technical lead was Mr. Brad Eppard. This report presents survival, behavioral, and fish passage results for tagged yearling Chinook salmon and juvenile steelhead as part of a survival study conducted at John Day Dam during spring 2011. This study was designed to evaluate the passage and survival of yearling Chinook salmon and juvenile steelhead to assist managers in identifying dam operations for compliance testing as stipulated by the 2008 Federal Columbia River Power System Biological Opinion and the 2008 Columbia Basin Fish Accords. Survival estimates were based on a paired-release survival model. iii Executive Summary Improving the survival rate of juvenile salmonids migrating downstream through the Federal Columbia River Power System (FCRPS) continues to be a high priority for the U.S. Army Corps of Engineers (USACE) and the region. Many of these fish are from populations listed as threatened or endangered under the Endangered Species Act of 1973. Increasing survival rates is necessary to ensure healthy salmon populations in the future and meet performance standards set forth in the 2008 Biological Opinion (BiOp) on configuration and 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 USACE Portland District (CENWP) is evaluating surface-flow outlets (SFOs) as a means to increase fish passage efficiency and in turn increase fish passage survival rates by reducing turbine passage of juvenile salmonids. The goal of this study was to provide fish passage and survival data necessary to evaluate the performance of the JDA prototype SFO, a top-spill weir (TSW), and the dam as a whole relative to the performance standards outlined in the BiOp and additional performance measures as stipulated in the Columbia Basin Fish Accords for yearling Chinook salmon (Oncorhynchus tshawytscha) and juvenile steelhead (O. mykiss). This study was conducted to provide the CENWP and regional fisheries managers with information necessary to assist with decision making for adaptively managing the configuration and operation of JDA to maximize the survival rates for juvenile salmonids. Researchers at the Pacific Northwest National Laboratory collaborated with the Pacific States Marine Fisheries Commission, CENWP, and the University of Washington to estimate survival rates and other performance measures for yearling Chinook salmon and juvenile steelhead passing through JDA during spring 2011. The original study design included evaluation of subyearling Chinook salmon in summer but river discharge far exceeded the 10-yr average halfway through the spring season and well into the summer, so the summer portion of this study was cancelled. The spring study was also divided into early season (April 27–May 16), where treatment discharge levels could be maintained and late season (May 16–May 29), when treatment discharge levels could not be managed. The objectives of this acoustic telemetry (AT) study of survival and passage at JDA were to estimate the following performance measures for yearling Chinook salmon and juvenile steelhead: • Survival: forebay to tailrace (BRZ-to-BRZ [boat-restricted zone]; 5 river kilometers [rkm], JDA forebay array to JDA dam face (2 rkm) and JDA dam face to JDA tailrace array (3 rkm)), dam passage to the JDA tailrace array (3 rkm), and dam passage by route to the JDA tailrace. • Travel times: forebay residence, tailrace egress, and project passage. • Passage metrics: fish passage efficiency, spill passage efficiency, and TSW passage efficiency. • Distributions: forebay horizontal approach distribution, forebay vertical distribution, and horizontal distribution by route and subroute. The current study was an official compliance test as outlined in the 2008 FCRPS BiOp. This study relied on releases of live juvenile salmonids double tagged with Juvenile Salmon Acoustic Telemetry System (JSATS) acoustic micro-transmitters (AMTs) and passive integrated transponders (PITs) in the Columbia River and used AT to evaluate the approach, passage, and survival of passing juvenile salmonids. Additional passage performance measures were also estimated, most of which were stipulated v in the Columbia Basin Fish Accords. Two spill discharge levels were also tested, 30% and 40%, to determine the effects of each independently on passage and survival metrics. A similar study conducted in 2010 at JDA verified that the dam face array performance was suitable for a full-scale compliance study in 2011, because detection probabilities were essentially 100% for both yearling Chinook salmon and steelhead and survival model assumptions were met. In the spring, 2,510 Yearling Chinook salmon and 2,587 juvenile steelhead surgically implanted with JSATS AMTs and PITs were released in the Columbia River upstream of JDA (rkm 390 near Roosevelt, Washington) and regrouped at the JDA face to form virtual releases. These releases were followed by downstream releases at two sites below JDA of 1,992 yearling Chinook salmon and 1,993 steelhead, which allowed for estimation of paired-release survival at JDA. Paired-release passage survival was estimated for fish passing through two river reaches: 1) the dam and 3 km of the tailrace and 2) the forebay (2 km), dam, and 3 km of the tailrace. The JSATS AMT model number SS130 weighing 0.438 g in air manufactured by Advanced Telemetry Systems and the Biomark HPT12 PIT were used in this investigation. This report provides a comprehensive summary of 2011 results, including route-specific passage survival estimates, travel times, and passage distributions. The study methods and results are summarized below (Table ES.1–Table ES.6). Table ES.1. Summary of methods and conditions at John Day Dam during 2011.