Biology, Behavior, and Resources of Resident and Anadromous Fish in the Lower Willamette River Final Report of Research, 2000-2004 Edited by Thomas A. Friesen Oregon Department of Fish and Wildlife 17330 Southeast Evelyn Street Clackamas, Oregon 97015 March 2005 Contracted by City of Portland Bureau of Environmental Services Endangered Species Act Program 1120 Southwest Fifth Avenue, Suite 1000 Portland, Oregon 97204 TABLE OF CONTENTS PREFACE………………………………………………………………………………………. 5 ACKNOWLEDGMENTS……………………………………………………………………… 5 SUMMARY……………………………………………………………………………………. .7 RECOMMENDATIONS ………………………………………………………………………12 Paper 1 – Description and Categorization of Nearshore Habitat in the Lower Willamette River…………………………………………………………………………………17 Paper 2 - Migratory Behavior, Timing, Rearing, and Habitat Use of Juvenile Salmonids in the Lower Willamette River..…………………………………………………….. 63 Paper 3 – Population Structure, Movement, Habitat Use, and Diet of Resident Piscivorous Fishes in the Lower Willamette River……………………………………………. .139 Paper 4 – Diets of Juvenile Salmonids and Introduced Fishes of the Lower Willamette River………………………………………………………………………………..185 Paper 5 – A Brief Survey of Aquatic Invertebrates in the Lower Willamette River….………223 3 4 PREFACE This document is the final report of research for a project funded by the City of Portland (COP) and conducted by the Oregon Department of Fish and Wildlife (ODFW). The general objective was to evaluate aquatic habitat and biotic communities in the lower Willamette River, and provide guidance for protecting species of threatened and endangered salmonids. Our report includes five research papers that describe how we addressed project hypotheses and objectives, how we reached our conclusions, and why we made our recommendations. The papers are listed and numbered in the Table of Contents, and the numbers are used to reference each paper in the Summary. The Summary integrates the results, conclusions, and recommendations, and provides the best overall picture of the status of aquatic resources in the lower Willamette River. The recommendations presented here were developed by the principal investigators, and will not necessarily be adopted as policies or guidelines by the Oregon Department of Fish and Wildlife. ACKNOWLEDGMENTS Many thanks to all the people who helped us accomplish our objectives over the past four years. The Portland Development Commission, the Portland Bureau of Environmental Services, the Portland Bureau of Development Services, and the Lower Willamette Group each contributed financial support for the project. Josh Allen, Chris Burnside, Sarah Courbis, Travis Eoff, Erin Phillips-Fincher, Ben Galuardi, Alex Gonyaw, J. T. Hesse, Michele Hughes, Jenny Kauffman, Jim Koloszar, Kathy Lisa, Casey Myers, Jodene Summers, Jason Vassar, Brian Vaughn, Mike Wallace, and Virgil Lee Watts of ODFW conducted much of the field sampling. Lisa Burner, Bonnie Cunningham, Ruth Farr, Jennifer Graham, and Howard Takata of ODFW co-authored annual reports and conducted field work. Matthew Powell and Joshua Tompkins of ODFW and Chad Smith of COP also assisted with field sampling. George Reed of ODFW purchased and maintained project equipment. Dave Ward of ODFW administered the project and provided expertise and guidance. John North of ODFW was instrumental in implementing the project, and served as project leader through 2001. Jim Middaugh, Mike Reed, and Chris Prescott of COP were project partners and provided detailed reviews of project design. Noah Adams, Scott Evans, John Plumb, Dennis Rondorf, Jamie Sprando, and Kenneth Tiffan of the U.S. Geological Survey provided expertise on radio telemetry design and techniques. Rick Boatner, Ken Bourne, Dick Caldwell, Milton Hill, Chris Kern, and Tom Rien of ODFW contributed time, supplies, equipment, and expertise. LTJG Katie Blanchard, CWO Robert Coster, and Captain G. F. Greene (U. S. Coast Guard); Karen Guntly (H. Naito Properties); Tony Lester, Brenda Strombo, and Alan Young (Multnomah County Department of Environmental Services-Transportation Division); Gene Loffler (Cargill Inc.); Jennifer Martinez (COP); and Mac Robinson (U. S. Army Corps of Engineers) provided facility access for radio telemetry fixed site locations; Skip and Joann White provided access at their residence for a radio telemetry fixed site. Dan Domina and Howard Bess (Portland General Electric); Captain Glenn Eisner (COP Fire Bureau); Jeff Jennings (Staff Jennings); and Sergeant Paul Steigleder (Clackamas County Sheriff Department) provided facility access for collection and holding of juvenile salmonids. Neil Bower, Terry Key, and Mike van den Tillaart of Lotek Engineering provided valuable assistance with radio telemetry. Mike Reed of COP, Dave Ward of ODFW, and Roger Peters of the U.S. Fish and Wildlife Service provided many helpful comments on earlier drafts of this report. 5 6 SUMMARY Paper 1 - Description and Categorization of Nearshore Habitat in the Lower Willamette River Our objective in this paper was to define and catalog existing nearshore fish habitat. We also identified habitat categories for subsequent analyses of fish use (Papers 2 and 3). Habitats were initially separated into six categories (beach, alcove, riprap, seawall, rock outcrop, and mixed) and 12 sub-categories based on their appearance and function. The majority (59.2%) of riverbank habitat in the study area (mouth to Willamette Falls) was undeveloped (“natural”), with no obvious modifications such as seawalls, riprap, or piers. Beaches were the most prevalent habitat type in the upper (above Ross Island Bridge; 38.8%) and lower (29.1%) sections of the study area, but the distribution of other types was considerably different. Undeveloped habitats composed 81.1% of the habitat in the upper section, but only 32.8% in the lower section. Nearshore structures (e.g., piers, docks, pilings) were associated with 18.7% of the total shoreline area. To provide a more quantitative approach to habitat categorization, we intensively surveyed 27 sites during spring, summer, autumn, and winter. We measured 60 physical or chemical parameters at each site, both instream and onshore. We then used cluster analysis and principal components analysis to group habitats and identify the parameters that contributed most to their separation. Sampling sites separated into five or six clusters in each season. Sites initially classified as seawall or rock outcrop always segregated into distinct groups. Sites described as beaches often occurred together in a group; riprap, rock, and mixed habitat types often appeared in multiple groups. These patterns increased our confidence that the initial groupings based on appearance were relatively accurate, and the multivariate analyses were useful in determining categories based on measured parameters. Bank vegetation, bottom substrate type, hydrology, and bank substrate type explained the majority of the variation in habitat data, and contributed most to the separation of sites into clusters. The percent of the bottom substrate composed of sand and onshore vegetation were important explanatory variables in every season; parameters important in at least two seasons included: river level, water depth, distance to the thalweg, transparency, bank slope, percent beach, percent small riprap, and percent bedrock. River chemistry (temperature, dissolved oxygen, and conductivity) varied little among sites during individual seasons, and did not contribute appreciably to site groupings. Paper 2 - Migratory Behavior, Timing, Rearing, and Habitat Use of Juvenile Salmonids in the Lower Willamette River Using electrofishing, beach seines, and radio telemetry, we assessed components of juvenile salmonid biology that would lead to a better understanding of their behavior in the lower Willamette River. We focused largely on nearshore habitat use, but also explored outmigration timing, size structure, growth, migration rate, and residence time. 7 Most (87%) juvenile salmonids we captured were Chinook salmon. Coho salmon and steelhead composed relatively small proportions of the catch (9% and 3%), and we occasionally observed mountain whitefish, sockeye salmon, and cutthroat trout. Hatchery-produced fish dominated the catch, composing 54% of the Chinook salmon, 66% of the coho salmon, and 91% of the steelhead. The electrofishing catch was dominated by large (>100 mm fork length) hatchery Chinook salmon; beach seines captured mostly small (≤100 mm fork length) Chinook salmon. Based on this gear selectivity and natural breaks in length frequencies, we assumed that Chinook salmon >100 mm fork length were yearlings (age 1) and smaller fish were subyearlings (age 0). Because we observed a large number of subyearling fish, and the abundance of fall Chinook salmon in the Willamette Basin is low, we concluded most small Chinook salmon in the lower Willamette River are spring-run fish that outmigrate as subyearlings. The outmigration period for Chinook salmon, both hatchery and unmarked, was surprisingly long. The presence of juvenile fish often increased in late autumn and persisted into the next summer, and juvenile salmonids were present in every month we sampled from May 2000 to July 2003. Winter and spring were clearly the periods of greatest abundance, though the presence of different races (spring and fall), size classes, and stocks undoubtedly confounded our ability to completely assess timing. Coho salmon and steelhead were generally present only during winter and spring. Median fork lengths and weights of hatchery