1) The purpose of this project is to measure changes in juvenile salmon habitat occurrence and health following restoration activities at the Mirror Lake Complex and Horsetail Falls in the Lower Columbia River and estuary. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NWFSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (e.g., the Lower Columbia River Estuary Partnership). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products to be produced include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland), the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger action effectiveness monitoring program overseen by the Estuary Partnership. 7) This is an ongoing project with a soft completion deadline; however, there are specific tasks to be completed on a yearly basis. Chinook salmon genetic stock identification.

1) The purpose of this project is to measure changes in juvenile salmon habitat occurrence and health following restoration activities at the Mirror Lake Complex and Horsetail Falls in the Lower Columbia River and estuary. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NWFSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (e.g., the Lower Columbia River Estuary Partnership). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products to be produced include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland), the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger action effectiveness monitoring program overseen by the Estuary Partnership. 7) This is an ongoing project with a soft completion deadline; however, there are specific tasks to be completed on a yearly basis. Chinook salmon genetic stock identification.

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU. 7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis. Growth rates of chinook salmon from Lower Columbia sites estimated from otolith analyses.

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU. 7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis. Fish catch composition, fish length and weight for Lower Columbia sites.

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU. 7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis. Fish catch composition, fish length and weight for Lower Columbia sites.

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU. 7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis. Prey composition in diet samples and water column tows at Lower Columbia River sites.

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU. 7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis. Concentrations of chemical contaminants in bodies and stomach contents of Chinook salmon from Lower Columbia sampling sites.

The goal of the tidal-fluvial estuary study is to determine the estuary's contribution to the spatial structure and life history diversity of Columbia River salmon stocks and the implications for estuary restoration. The study targets salmon use of tidal-fresh habitats in the estuary from Rkm 75 to Bonneville Dam, and addresses four primary objectives: 1. Characterize the temporal and spatial distribution of Chinook salmon genetic stock groups throughout the estuary (March 2010 - March 2012). 2. Determine stock-specific habitat use, life histories, and performance of juvenile salmon in key habitat complexes to fill data gaps in the tidal fluvial reaches of the estuary (2012-2016). 3. Monitor juvenile salmon life histories and their contributions to adult returns in selected estuary tributaries, including tributary examples where tidal habitats have been restored (2012-2018). 4. Evaluate estuary restoration needs for recovery of all salmon ESUs and account for projected effects of climate change through application of a salmon life-cycle model (2011-1015). The study, funded by the U.S. Army Corps of Engineers, involves a large team of researchers organized by NOAA Fisheries, including researchers from the Oregon Health and Sciences University, University of Washington, and Washington Department of Fish and Wildlife. The study addresses critical uncertainties identified in the research, monitoring, and evaluation (RME) program for the Federal Columbia River Estuary Program (FCREP). The Estuary Program is intended to conserve and restore the estuary ecosystem to improve the performance of listed salmonid populations. Products from the tidal-fluvial study will include: 1. Descriptions of stock-specific temporal and spatial distributions of Chinook salmon throughout the estuary. 2. Estimates of variations in Chinook salmon stock composition and stock-specific growth, food habits, consumption rates, and bioenergetic efficiencies within selected tidal-fluvial habitats. 3. Estimated contributions of estuarine life histories among returning adult Chinook salmon from selected populations throughout the Columbia River Basin. 4. A hydrological model quantifying the dynamics of rearing habitat opportunities for juvenile salmon at estuary reach and habitat scales. 5. Improved life-cycle models to account for the estuarine life histories of juvenile salmon and estimating the potential effectiveness of estuary restoration actions on the recovery and viability of selected salmon stocks. These results will directly address information needs to support estuary actions specified in the Federal Columbia River Power System (FCRPS) Biological Opinion for the Columbia River. The tidal-fluvial estuary study is part of an ongoing estuary research program initiated in 2002. The current study expands upon earlier research conducted in the lower 100 km of the estuary from 2002 to 2008. Although all objectives will be addressed by 2018 to correspond with a review of progress implementing the FCRPS Biological Opinion, some sampling activities may extend beyond this date to allow brood-year reconstruction of estuary contributions to adult returns in selected streams (Objective 3). Bimonthly genetic stock group distribution for juvenile Chinook Salmon collected from 3 habitats each from 6 tidal-fluvial estuary reaches and monthly fish species composition, abundance, and length:weight; Chinook salmon life history and genetic stock ID.

This project evaluates data from coded wire tagging with that from parental based tagging to identify stock of origin for Chinook salmon landed in Washington state commercial troll fishery.

This is a long-term (30-year) NWFSC Genetics and Evolution Program study to monitor the genetic characteristics and population dynamics of hatchery- and natural-origin Chinook salmon and steelhead in the Snake River Basin, which are both species listed as threatened under the US Endangered Species Act. Genetic tools are used to determine if naturally spawning hatchery fish are influencing the adaptive potential and viability of wild fish in the basin. This work involves long-term annual field work to collect DNA from threatened Chinook salmon and steelhead at numerous locations throughout the Snake and Salmon River Basin and analyze the genetic signatures from the collections in the context of a long-term historical baseline of hatchery production and natural variation in wild salmonid production there. Initiated in 1989, this study monitors genetic changes associated with hatchery propagation in multiple Snake River sub-basins for Chinook salmon and steelhead. We also derive estimates of reproductive success for individual families and groups of fish. The information obtained from this study directly addresses a critical knowledge gap identified by comanagers, which is: under what conditions does hatchery supplementation provide a sustained contribution to natural production? Co-managers are ODFW, CTUIR, NPT, WDFW, IDFG, and SBT. This type of monitoring work is now an essential part of hatchery reform and the goal of using widespread hatchery propagation in recovery of natural populations.