Multi-scale action effectiveness research in the lower Columbia River and estuary, 2012: Final annual report

PNNL-22481\nPrepared for the U.S. Army Corps of Engineers, Portland District,\nUnder an Interagency Agreement with the U.S. Department of Energy\nContract DE-AC05-76RL01830\nMulti-Scale Action Effectiveness\nResearch in the Lower Columbia\nRiver and Estuary, 2012\nFINAL ANNUAL REPORT\nPacific Northwest National Laboratory\nOregon Department of Fish and Wildlife\nNational Marine Fisheries Service\nUniversity of Washington\nU.S. Fish and Wildlife Service\nNovember 2013\nDISCLAIMER\nThis report was prepared as an account of work sponsored by an agency of the\nUnited States Government. Neither the United States Government nor any agency\nthereof, nor Battelle Memorial Institute, nor any of their employees, makes any\nwarranty, ext>ress or implied, or assumes any legal liability or res1>onsibility\nfor the accuracy, com1lleteness, or usefulness of any information, a1>1>aratus,\nt>roduct, or t>rocess disclosed, or re1>resents that its use would not infringe\nt>rivately owned rights. Reference herein to any specific commercial product,\nprocess, or service by tr'dde name, tr'ddemark, manufacturer, orothenvise does not\nnecessarily constitute or imply its endorsement, reconunendation, or favoring by\nthe United States Government or any agency thereof, or Battelle MemoriaJ\nInstitute. The views and opinions of authors expressed herein do not necessarily\nstate or reflect those of the United States Government or any agency thereof.\nPACIFIC NORTHWEST NATIONAL LABORATORY\noperated by\nBATTELLE\nfor the\nUNITEDSTATESDEPARTMENTOFENERGY\nunder Contract DE-AC05-76RLOJ830\nPr-intt.'fl in the United States of AmeJiCl\\\nAvailable to DOE and DOE contr-actor-s fmm the\nOffice of Scientific and Tech.niCl\\1 lnfor·mation,\nP.O. Box 62, Oak Ridge, TN 37831-0062;\nph: (865) 576-8401\nfax: (865) 576-5728\nemail: r-epor1s@adon.is.osti.gov\nAvailable to the public li·orn the National Teclm.icallnfonnation Ser·vice\n5301 Shawnee Rd., Alexandria, VA 22312\nph: (800) 553-NTIS (6847)\nemail: ordei'S(@JJtis.gov <http://www .ntis.gov/about/lonn.aspx>\nOnline or·der-ing: http://www .ntis.gov\n@ Tlus document was printed on recycled paper.\n(8/2010)\nPNNL-22481\nMulti-Scale Action Effectiveness\nResearch in the Lower Columbia\nRiver and Estuary, 2012\nFINAL ANNUAL REPORT\nGE Johnson T Brewer2\nNK Sather AJ Bryson\nAJ Storch1 EM Dawley\nJ Johnson2 DR Kuligowski4\nJR Skalski3 T Whitesel2\nDJ Teel4 C Mallette1\nNovember 2013\nPrepared for\nU.S. Army Corps of Engineers, Portland District\nunder an Interagency Agreement with the U.S. Department of Energy\nPacific Northwest National Laboratory\nRichland, Washington 99352\n1 Oregon Department of Fish and Wildlife, Portland, Oregon\n2 U.S. Fish and Wildlife Service, Vancouver, Washington\n3 University of Washington, Seattle, Washington\n4 National Marine Fisheries Service, Seattle, Washington\nPNNL-22481\niii\nPreface\nPacific Northwest National Laboratory (PNNL), the National Marine Fisheries Service (NMFS), the\nOregon Department of Fish and Wildlife (ODFW), the University of Washington (UW), and the U.S. Fish\nand Wildlife Service (USFWS) conducted this study for the U.S. Army Corps of Engineers, Portland\nDistrict (USACE). The study was coordinated regionally under the USACE’s Anadromous Fish\nEvaluation Program, study code EST-P-11-01. The goal of the study was to evaluate the ecological\nbenefits of restoration actions for juvenile salmon in the lower Columbia River and estuary (LCRE;\nrkm 0–234). The PNNL project manager was Gary Johnson. The USACE technical lead was Cynthia\nStudebaker. For more information about the study, please contact Cynthia Studebaker (503 808 4788).\nThis study originated with research funded by the Bonneville Power Administration (BPA) on\njuvenile salmon ecology in tidal freshwater during 2007–2010. In 2010, the project was transferred from\nBPA to the USACE under provisions of the Washington Memorandum of Agreement for estuary habitat\nrestoration. The first annual report (2011) for the USACE-funded work was delivered in 2012. The\npresent annual report is the second in the USACE series.\nSuggested citation for this report:\nJohnson GE, NK Sather, AJ Storch, J Johnson, JR Skalski, DJ Teel, T Brewer, AJ Bryson, EM Dawley,\nDR Kuligowski, T Whitesel, C Mallette. 2013. Multi-Scale Action Effectiveness Research in the Lower\nColumbia River and Estuary, 2012. PNNL-22481, final annual report submitted to the U.S. Army Corps\nof Engineers, Portland District, Portland, Oregon, by Pacific Northwest National Laboratory, Richland,\nWashington.\nv\nAcknowledgments\nThis study was made possible by contributions made by many individuals to whom we extend our\ngratitude. Jan Salter (PNNL) managed the contracts. The U.S. Forest Service allowed property access to\nsites at the Sandy River delta. From PNNL, Sarah Aspens and Cynthia Wright provided data collection\nand management support. Susan Ennor and Kathy Neiderhiser edited and formatted the report,\nrespectively; Shon Zimmerman, Matt Hennen, and James Hughes were instrumental in the acoustic\ntelemetry study. We especially acknowledge the dedication and hard work put forth in the field by\nElizabeth Torrey from ODFW. Funding for the study was provided by the USACE under the\nCongressionally-appropriated Columbia River Fish Mitigation project.\nvii\nExecutive Summary\nThe study reported herein was conducted for the U.S. Army Corps of Engineers, Portland District\n(USACE) by researchers at the Pacific Northwest National Laboratory (PNNL), National Marine\nFisheries Service (NMFS), Oregon Department of Fish and Wildlife (ODFW), University of Washington\n(UW), and U.S. Fish and Wildlife Service (USFWS). The goal of the study was to evaluate the ecological\nbenefits of restoration actions for juvenile salmon in the lower Columbia River and estuary (LCRE;\nrkm 0–234).\nThis multi-year study (2011–2018) addresses the ecological benefits of restoration actions at multiple\nspatial scales over time. The spatial scales include the 1) site scale as a result of an individual project,\n2) landscape scale as a result of multiple restoration actions located within a ~50-km segment of the\nLCRE, and 3) estuary scale as a result of the cumulative effects of multiple restoration actions estuary-wide.\n2012 Objectives\nObjective 1, Site Scale – a) Continue pre-restoration action effectiveness research to evaluate effects\nof the upcoming dam removal/rechannelization at the Sandy River delta; b) continue post-restoration\naction effectiveness research to evaluate effects of the tide gate replacements at the Julia Butler Hansen\nNational Wildlife Refuge (JBHNWR) mainland and Tenasillahe Island.\nObjective 2, Landscape Scale – a) Estimate juvenile salmon density in shallow water habitats between\nSt. Helens and Longview (rkm 110–141); b) estimate residence time for tagged juvenile Chinook salmon\nduring winter 2012 in Carroll’s Channel behind Cottonwood Island.\nObjective 3, Estuary Scale – Prepare a compendium of tag release-recapture technologies to inform\nplanning for future action effectiveness studies.\nSummary of Findings\nThe following summary of findings for the 2012 Multi-Scale Action Effectiveness study is organized\nby the objectives. The study period is October 2011 through December 2012, unless noted otherwise.\nObjective 1, Site Scale\nSandy River delta – Continue pre-restoration action effectiveness research to evaluate effects of the\nupcoming dam removal/rechannelization at the Sandy River delta.\n• Environmental conditions during the study period entailed low flow conditions (75–125 kcfs) that\npersisted from late summer through fall. Peak discharge (350–450 kcfs) occurred from spring to\nsummer months. Within a given season, variability in both water-surface elevation and water\ntemperature was observed among the four Sandy River delta sites, especially when river discharge\nwas low.\n• Fish community composition during the study period consisted of 27 species, of which 15 were non-native\nfishes. In terms of total numbers of fish, catches predominantly comprised native taxa;\nviii\nnon-native constituents accounted for approximately 16% of the total catch. Threespine stickleback\ncomposed 90% of the total number of fish sampled.\n• Three species of unmarked and marked salmon were captured: chum, coho, and Chinook. Unmarked\nChinook salmon were the only species captured during every season and the most abundant salmon\nspecies captured. Seasonally, the lowest mean densities for unmarked Chinook salmon (<0.002\nfish/m2) occurred during fall; the highest densities (~0.015 fish/m2) were observed during winter.\n• The lengths of juvenile salmon captured ranged from 33 to 127 mm fork length. Seasonally, the\nsmallest mean size of all salmonids occurred during winter (65 mm) and the largest occurred during\nfall 2011 (96 mm). Unmarked Chinook salmon primarily comprised fry size fish (<60 mm) during\nwinter months, with size classes <100 mm present during spring. Overall, the sizes of unmarked\nChinook salmon sampled at the Sandy River delta increased during summer and fall months.\n• Stock composition estimates from the genetics analysis of 192 unmarked Chinook salmon sampled in\nthe Sandy River delta showed that most fish were from the Spring Creek Group Tule Fall (39%) and\nthe Upper Columbia Summer/Fall (33%) stock groups. Smaller proportions were estimated for the\nWillamette River Spring (8%), West Cascade Tributary Fall (7%), Snake River Fall (6%), West\nCascade Tributary Spring (5%), Deschutes River Fall (1%), and Mid and Upper Columbia River\nSpring (1%) stock groups. Most marked Chinook salmon were from the Upper Columbia\nSummer/Fall (56%) and the Spring Creek Group Tule Fall (36%) stock groups.\n• The diets of juvenile Chinook salmon were dominated by dipterans (primarily chironomids and\nceratopogonids) and amphipods. Of these prey taxa, dipterans were most frequently consumed in\nlarge

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