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. Catch composition and salmon density.

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. Juvenile chinook salmon diet composition and prey availability in habitat.

Sampling juvenile salmon and associated fishes in open waters of the lower Columbia River estuary. Field work includes bi-weekly sampling during the spring outmigration (Apr-June), and monthly sampling throughout the summer and fall. We use a purse seine to sample open water habitats. Our objectives are to document the seasonal and interannual variation in juvenile salmon immediately prior to ocean entry, with respect to abundance, size, origins (H/W), stocks, food habitats, and parasites/pathogens. We also document the larger estuarine fish community, which serves a critical role as prey for juvenile salmon predators. Abundance and size of fish caught in Columbia estuary.

Field data for fishes sampled using bottom gill nets and otter trawls during daylight hours in the northern part of the Sacramento-San Joaquin Delta, California, USA. Two adjacent tidal wetlands were targeted for sampling: Little Holland Tract and Liberty Island Conservation Bank

Field data for fishes sampled using bottom gill nets and otter trawls during daylight hours in the northern part of the Sacramento-San Joaquin Delta, California, USA. Two adjacent tidal wetlands were targeted for sampling: Little Holland Tract and Liberty Island Conservation Bank

Comprehensive planning and monitoring of abiotic (hydrology, land forms, energy and nutrients, and chemistry) and biotic (plants, fish, invertebrates, birds, mammals) attributes pre- and post-breach at a 150 hectare site in the Snohomish estuary. LiDAR and orthophotos from 2009 across whole Snohomish River estuary.

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). PIT detection data (residence time, travel time) in estuary wetland channels from juvenile salmon tagged by this project and other projects.

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. Chemical contaminants in chinook salmon bodies.

Comprehensive planning and monitoring of abiotic (hydrology, land forms, energy and nutrients, and chemistry) and biotic (plants, fish, invertebrates, birds, mammals) attributes pre- and post-breach at a 150 hectare site in the Snohomish estuary. RTK GPS point locations at project and reference sites.

Relatively little scientific research or monitoring has occurred in the Pacific Northwest or elsewhere on the biological effectiveness of restoration efforts in heavily urbanized watersheds. With the overarching goal of improving ecological health of its urban creeks, the City of Seattle is testing innovative approaches to stormwater management. We report here on four years of pre-project monitoring data collected over 2006-2009 for one such technique: Natural Drainage Systems (NDS). This low-impact development approach is designed to modify the quantity, quality, and timing of stormwater delivery to creeks and other water bodies. Seattle Public Utilities has proposed a large-scale NDS within the Pipers Creek basin of North Seattle that will treat approximately 60% of the Venema Creek sub-basin. The focus of NOAAs research effort has been to develop appropriate monitoring parameters and collect baseline data to evaluate the effectiveness of this major restoration action. Our selection of study parameters was guided by specific project goals and includes measures of physical habitat, contaminant loading, and in-stream biota. We found that the biological health of Pipers Creek is poor compared to forested streams in the Puget Sound region, but comparable to other urban streams in the City of Seattle. The fish community is dominated by cutthroat trout Oncorhynchus clarki; scores for the benthic index of biological integrity (B-IBI) range from very poor to poor; and diatom assemblages are composed of a relatively high proportion of species tolerant of high nutrient levels, organic enrichment, and sedimentation. Despite poor stream health, densities of cutthroat trout in three of our five study reaches were higher than many urban streams and approaching densities of cutthroat found in natural streams. This may be due to the migratory nature of cutthroat trout, as about half these fish were detected migrating from our study area to lower Piper Creek or Puget Sound. Results from heavy metal sampling were inconsistent. Zinc concentrations in soil, black fly larvae, and mayfly nymphs collected from Pipers Creek study reaches were significantly higher than for forested streams. We did not detect any differences in copper concentrations between urban and non-urban streams. We hypothesize that in-stream biological health will improve relative to current baseline conditions following Venema NDS implementation, with treated reaches beginning to more closely resemble forested conditions. Based on statistical power analyses, we recommend that post-project monitoring focus on rate and taxonomic composition metrics rather than simple density measurements. Given the City of Seattles considerable investment of restoration funds towards NDSs, it is critical that post-project data be collected so as to explicitly test these hypotheses. Habitat typing, channel geometry, substrate, temperature.