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1 The contribution of tidal fluvial habitats in the Columbia River Estuary to the recovery of diverse salmon ESUs Curtis Roegner1,Daniel Bottom1, Antonio Baptista2, Lance Campbell3, Andrew Claiborne3,Kurt Fresh1, Susan Hinton1, Regan McNatt1, Charles Simenstad4, David Teel1, Rich Zabel1 Report of research by Fish Ecology and Conservation Biology Divisions Northwest Fisheries Science Center National Marine Fisheries Service National Oceanographic and Atmospheric Administration 2725 Montlake Blvd. E. Seattle, Washington 98112-2097 for Portland District Northwestern Division U.S. Army Corps of Engineers P.O. Box 2946 Portland, Oregon 97208-2946 May 2013 1NOAA Fisheries, Northwest Fisheries Science Center 2Oregon Health and Science University 3School of Aquatic and Fisheries Sciences, University of Washington 4Washington Department of Fish and Wildlife2 INTRODUCTION AND STUDY OBJECTIVES The 2008 Biological Opinion on Operation of the Federal Columbia River Power System established estuary restoration goals for ten-year survival improvements of 9% for ocean-type and 6% for stream-type ESUs. To support these goals, a qualitative assessment process (Columbia River Estuary Recovery Plan Module) was devised to identify limiting factors and to prioritize estuary restoration actions based on their presumed survival benefits. The method ranks the potential benefits of various restoration projects based on published results and professional judgments about their relative effectiveness. Empirical estimates of survival benefits are unavailable, however, and the actual contributions of single or cumulative estuary actions to the survival goals in the Biological Opinion are unknown. Today scores of wetland restoration projects have been undertaken in the estuary as a method to recover at-risk salmon populations throughout the Columbia River basin, based in part on the latest information about the estuary’s role as a productive nursery ground for juvenile salmon (Bottom et al. 2005

Our studies in the lower 100-km of the Columbia River estuary quantified historical habitat changes and provided new information about contemporary abundance patterns, life histories, and habitat associations of Chinook salmon. The conceptual framework for this research defined salmon performance in the estuary as the product of three factors: habitat opportunity, habitat capacity, and the structure/life histories of source populations. Our 2002-2008 survey results provided empirical data to support this framework by quantifying Chinook salmon performance in terms of temporal abundance, life history and stock-group diversity, foraging success, and growth, as well as by quantifying the relationships between stock groups and one or more of these factors. In Part I, we detail our reconstruction of historical habitat opportunities and changes in the estuary as influenced by the tide, river flows, and temperature. In Part II, we depict contemporary habitat opportunities based on present-day patterns of salmon distribution and abundance and upon various physical factors that influence fish access to shallow-water rearing areas. In Part III, we compare the capacity of different wetland and nearshore habitats in supporting juvenile Chinook salmon as indicated by variations in prey availability, salmon diet, and rates of consumption. Finally, in Part IV, we examine the effects of upriver population structure and life histories on estuary rearing behavior and performance, including the genetic sources of individual Chinook salmon found within particular habitats and stock-specific patterns of residency and growth. These surveys provided new information about the present estuarine habitat associations of juvenile salmon. They also provided data for estimates of historical change in habitat conditions, estimates of historical change in salmon life histories, and analyses of food webs. Below we summarize major conclusions drawn from these evaluations., Prepared in collaboration with the Institute of Environmental Health, Oregon Health and Science University, Beaverton, the School of Aquatic and Fishery Science, University of Washington, Seattle, the Washington Department of Fish and Wildlife, Olympia, the Department of Civil and Environmental Engineering, Portland State University, Portland, OR, and the Pacific States Marine Fisheries Commission, Portland, OR.

Estuarine Habitat and Juvenile Salmon: Current and Historical Linkages in the Lower Columbia River and Estuary Final Report 2002-2008 Daniel L. Bottom,1 Antonio Baptista,2 Jennifer Burke,3 Lance Campbell,4 Edmundo Casillas,1 Susan Hinton,1 David A. Jay,5 Mary Austill Lott,3 George McCabe,6 Regan McNatt,1 Mary Ramirez,3 G. Curtis Roegner,1 Charles A. Simenstad,3 Sarah Spilseth,3 Lia Stamatiou,3 David Teel,1 and Jeannette E. Zamon1 Report of research by 1Fish Ecology Division, Northwest Fisheries Science Center U.S. National Marine Fisheries Service National Oceanic and Atmospheric Administration 2725 Montlake Blvd. E. Seattle, Washington 98112 to U.S. Army Corps of Engineers Portland District 333 SW First Avenue Portland, Oregon 97208-2946 Contract W66QKZ20374382 December 2011 __________________________ 2 Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 3 School of Aquatic and Fishery Science, University of Washington, Seattle, WA 4 Washington Department of Fish and Wildlife, Olympia, WA 5 Department of Civil and Environmental Engineering, Portland State University, Portland, OR 6 Pacific States Marine Fisheries Commission, Portland, OR ii iii EXECUTIVE SUMMARY Our studies in the lower 100-km of the Columbia River estuary quantified historical habitat changes and provided new information about contemporary abundance patterns, life histories, and habitat associations of Chinook salmon. The conceptual framework for this research defined salmon performance in the estuary as the product of three factors: habitat opportunity, habitat capacity, and the structure/life histories of source populations. Our 2002-2008 survey results provided empirical data to support this framework by quantifying Chinook salmon performance in terms of temporal abundance, life history and stock-group diversity, foraging success, and growth, as well as by quantifying the relationships between stock groups and one or more of these factors. In Part I, we detail

This Final Technical Report discusses the accomplishments of an effort to support NASA and FAA goals for visualization of the National Airspace System (NAS) to aid the analysis of proposed changes to increase its capacity and meet future needs. The Air Force Research Laboratory (AFRL) is developing a JView-based visualization tool, known as the Viewer, for visualizing objects and results from NASA's ACES (Airspace Concept Evaluation System) simulation application. IV4D (Interactive Visualization in 4-D) was developed as a plug-in to the Viewer. It employs a combination of heuristics and visualization defaults in order to search for entities to visualize, and then to display them with minimal user selection. IV4D makes it easy for aeronautics researches and others to display flight trajectories, airspace boundaries, weather, and more, with data coming from multiple sources, including multiple software and simulation applications. IV4D is designed to work with most forms of NAS state data, concentrating first on data representing the most common elements of objects within the NAS - positioned still and moving objects; that is, concentrating on objects situated by latitude, longitude, elevation, which are present for a defined period of time., The original document contains color images.

BENTIUC AND EPIBENTHIC INVE RTEBRATES, FISHES, AND SEDIMENTS AT AND ADJACENT TO A PROPOSED NEW SITE FOR AREA D, AN IN-WATER DREDGED-MATERLA.L DISPOSAL SITE IN THE LOWER COLUMBIA RIVER, 1991 by George T. McCabe, Jr. Susan A. Hinton and Robert L. Emmett Final Report Funded by U.S. Army Corps of Engineers Portland District P.O. Box 2946 Portland, Oregon 97208 (Contracts E96910017 and E96910040) and Coastal Zone and Estuarine Studies Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2725 Montlake Boulevard East Seattle, Washington 98112 March 1993 CONTENTS Page INTRODUCTION .................................... - ...... I METHODS ............................................... .... 3 Sampling .............. ................................. 3 Benthic Invertebrates and Sediments ..................... 3 Fishes, Dungeness Crabs, and Shrimps .......... ......... 4 Data Analyses ........... ........ ....................... 6 Benthic Invertebrates ............. ................... 6 Fishes, Dungeness Crabs, and Shrimps .................... 7 Sediments .......................................... 7 RESULTS ..................................................... 7 Benthic Invertebrates ....................................... 7 Fishes, Dungeness Crabs, and Shrimps .................. ...... 13 Sediments ............................................... 18 DISCUSSION ....................... .......................... 24 CONCLUSIONS AND RECOMMENDATIONS ....... ................. 25 ACKNOWLEDGMENTS .......................... ............... 26 REFERENCES .................. ....... ...................... 27 APPENDIX .................................. ................. 28 INTRODUCTION The U.S. Army Corps of Engineers (COE), Portland District, is responsible for maintaining navigation channels in the Columbia River estuary. This responsibility requires annual dredging and disposal of millions of cubic yards of bottom s

BENTHIC INVERTEBRATES AND SEDIMENTS IN VEGETATED AND NONVEGETATED HABITATS AT THREE INTERTIDAL AREAS OF THE COLUMBIA RIVER ESTUARY, 1992 by George T. McCabe, Jr. and Susan A. Hinton Report of Research Funded by U.S. Army Corps of Engineers Portland District P,O. Box 2946 Portland, Oregon 97208 (Contract E9592012) and Coastal Zone and Estuarine Studies Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2725 Montlake Boulevard East Seattle, Washington 98112-2097 August 1993 CONTENTS Page INTRODUCTION ................................. ............. 1 MET1IODS ................................ ................... 2 Sampling ................. .............. .......... 2 Data Analyses ............... ....... ............. ...... 2 RESULTS .......... .......................................... 5 Benthic Invertebrates. . @ . @ . . @ ............................... 5 Sediments ............................................... 10 DISCUSSION ....... ............................ .... 12 ACKNOWLEDGMENTS .......................................... 14 REFERENCES ................................................. 15 APPENDIX .................................................... 17 INTRODUCTION The physical characteristics of the Columbia River estuary have been altered considerably by man during the last century. Major changes in the estuary were caused by such activities as jetty and pile-dike construction, diking of swamps and marshes, dam construction and operation, dredging, fillin,-, and island construction (Sherwood et al. 1990). Deepening and maintenance of the navigation channel in the estuary have resulted in the creation of islands, including Miller Sands, Jim Crow Sands, and Rice Island. Miller Sands, Jim Crow Sands, and Rice Island were created from material dredged from the navigation channel and are located in the same general area of the Columbia River estuary; however, the intertidal areas of these

BENTHIC INVERTEBRATES, DEMERSAL FISHES, AND SEDIMENT CHARACTERISTICS AT AND ADJACENT TO OCEAN DREDGE MATERIAL DISPOSAL SITE F, OFFSHORE FROM THE COLUMBIA RIVER, JUNE 1989 AND 1990 by Susan A. Hinton Robert L. Emmett and George T. McCabe, Jr. Final Report Funded by U.S. Army Corps of Engineers Portland District P.O. Box 2946 Portland, Oregon 97208 (Contract E8689AI50) and Coastal Zone and Estuarine Studies Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2725 Montlake Boulevard East Seattle, Washington 98112-2097 June 1992 iii CONTENTS Page INTRODUCTION ............................................................. 1 METHODS .................................................................. I Sampling ........................................................... I Benthic Invertebrates and Sediments .......................... I Fishes and Large Epibenthic Invertebrates .................... 3 Data Analyses ...................................................... 4 Benthic Invertebrates ........................................ 4 Fishes and Large Epibenthic Invertebrates .................... 5 Sediments .................................................... 5 RESULTS .................................................................. 6 Benthic Invertebrates .............................................. 6 Fishes and Large Epibenthic Invertebrates .......................... 9 Sediments .......................................................... 14 DISCUSSION ............................................................... 19 CONCLUSIONS .............................................................. 20 ACKNOWLEDGMENTS ......................................................... 21 LITERATURE CITED ......................................................... 22 APPENDIX ................................................................. 23 INTRODUCTION In 1989, the U.S. Army Corps of Engineers (COE) agreed to assis

BENTHIC INVERTEBRATES AND SEDIMENT CHARACTERISTICS IN SUBTIDAL HABITAT AT RICE ISLAND, COLUMBIA RIVER ESTUARY, DECEMBER 1991 AND MARCH 1992 by Susan A. Hinton Robert L. Emmett and George T. McCabe, Jr. Final Report Funded by U.S. Army Corps of Engineers Portland District P.O. Box 2946 Portland, Oregon 97208 (Contract E96920018) and Coastal Zone and Estuarine Studies Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2725 Montlake Boulevard East Seattle, Washington 98112 October 1992 CONTENTS Page INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . 1 METHODS . . . . . . . . . . . . . . . . . . . . . . . . . 2 Sampling . . . . . . . . . . . . . . . . . . . . . . 2 Data Analyses . . . . . . . . . . . . . . . . . . . 5 Benthic Invertebrates . . . . . . . . . . . . . 5 Sediments . . . . . . . . . . . . . . . . . . . 5 RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . 6 Benthic Invertebrates . . . . . . . . . . . . . . . 6 Sediments . . . . . . . . . . . . . . . . . . . . . 8 DISCUSSION . . . . . . . . . . . . . . . . . . . . . . . 8 ACKNOWLEDGMENTS . . . . . . . . . . . . . . . . . . . . . 12 LITERATURE CITED . . . . . . . . . . . . . . . . . . . . 14 APPENDIX . . . . . . . . . . . . . . . . . . . . . . . . 15 INTRODUCTION The U.S. Army Corps of Engineers (COE) Portland District is responsible for annually dredging and disposing of more than 2 million yd' (1.5 million M3) of bottom sediments from the navigation channel between River Miles (RM) 4.4 and 28.8 in the Columbia River estuary. Existing island and shoreline dredged-material disposal sites are nearly filled to capacity, and options for new disposal sites for such large volumes of dredged material are extremely limited. One potential disposal site is the area just north of Rice Island, an island created with dredged material. Proposals for expanding Rice Island with dredged material include creating a 10,000-ft (3,048-m) by 500