The goal of the Trinity River project is to identify the potential positive effects of large-scale restoration actions in a 63 kilometer reach of the Trinity River below Lewiston Dam, in the hope of guiding on the ground restoration actions. River restoration plans often propose numerous rehabilitation actions to address key habitat impairments for salmonids. However, restoration plans rarely propose alternative sets of actions or attempt to quantify the potential benefits to targeted biota. In this paper, we use geomorphic and biological analyses to estimate restoration potential for each of 37 reaches in a 64-km section of Trinity River, California, from the North Fork Trinity River to Lewiston Dam (the focus of habitat rehabilitation efforts under the Trinity River Restoration Program). We first predicted the channel pattern that might develop based in each reach on slope-discharge criteria, and then used these potential patterns along with floodplain width to estimate the maximum sinuosity that restoration actions could likely achieve, as well as a maximum side-channel length that might be created in each reach. For each scenario, we then used existing stream habitat and juvenile salmonid data from previous studies in the Trinity River and other watersheds to determine current and restored carrying capacity. Potential increases in Chinook and steelhead carrying capacity range from 39% for a relatively realistic estimate of increasing habitat quality (more low velocity areas with cover) to 67% for a more optimistic scenario that increases both sinuosity and habitat quality. Only the most optimistic scenario that increases habitat quality, increases sinuosity, and constructs tens of kilometers of side channels more than doubles potential juvenile salmonid production (140% increase). These quantitative predictions provide a frame of reference for evaluating alternative restoration options, and for setting measureable restoration goals. Database of stream reach attributes.

Basin-wide analysis of potential to improve tributary habitats in the Columbia River basin through restoration of habitat-forming processes. Identification of geomorphological target conditions for river restoration is typically based on locally measured reference conditions, yet few reference sites remain in much of the 630,000 km2 Columbia River Basin, USA. Therefore, we predicted reference conditions throughout the basin based on key reach-scale variables, which we empirically derived from a limited number of reference sites. We developed a GIS data set that depicts pre-settlement riparian vegetation in the Columbia River Basin to guide stream restoration for endangered salmon. However, the modeled riparian species composition was quite inaccurate, so we are not distributing these model results. Methods: We first created a data layer of historic riparian vegetation information from survey notes that were taken mid-19th to early 20th century during the Public Land Survey System (PLSS) conducted by General Land Office (GLO). Our reconstructed riparian vegetation data include randomly sampled basin-wide data (drainage area 200,000 km2), as well as intensively reconstructed watershed-level data (3,000 km2). Second, based on the reconstructed riparian vegetation points, which are arrayed along a 1-mile (1600 m) grid, we are developing statistical models to estimate potential historic riparian vegetation types (conifer, hardwood, willow-shrub, grass, sage) as well as the probability of occurrence of individual species at stream reach level (~ 200 m) in the basin. We examined environmental variables, such as mean annual precipitation, average minimum and maximum temperature, channel gradient, channel bankful width, floodplain width, and fine sediment supply potential, against five vegetation types and found that precipitation and temperature discriminate vegetation groups. We also developed vegetation response curves against each variable, using kernel density estimates to describe the probability of each vegetation type occurring across the range of each environmental variable. GIS hydrography layer with riparian attributes.

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 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.

NOAA has designed and is currently implementing a hyporheic monitoring plan for the Thornton Creek watershed in North Seattle. This work is being conducted for Seattle Public Utilities, who in 2015 completed two large-scale floodplain reconnection projects in the Thornton Creek Watershed. This study will evaluate restoration effectiveness by comparing control and treatment study reaches to each other and to forested references streams before and after restoration. NOAAs data collection focuses on hyporheic invertebrates, water temperature, and nutrient concentrations. Taxonomic and density data for aquatic invertebrates collected at project sites.

The goals of this project are to examine 1) the relative importance of multiple aquatic habitats (streams, estuaries, and nearshore areas, for example) used by salmon during their migration, 2) evaluate how different forms of density dependence influence the relative importance of these habitats, and 3) determine the influence of life history variation on extinction risk. Analyses of Skagit Chinook, OR coho, and Winter run Chinook are currently being examined. Results of GIS models of habitat capacity for Sacramento Winter run Chinook salmon.

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.

This study evaluates system-level effects of several estuary restoration projects on juvenile Chinook salmon production in the Skagit River estuary. The monitoring encompasses juvenile out-migration from rivers, estuary rearing, and shoreline and subtidal neritic residency. NWFSC is responsible for sampling neritic systems. Excel spreadsheets and Filemaker Pro databases.

By engaging 30 reserves from across the country in habitat mapping, this project highlighted differing trends among regions and estuarine habitat types. Working with local and national end users, including the NERRs and a variety of organizations interested in understanding estuarine habitat change, the project built a shared understanding of trajectories of change to design and build support for future restoration strategies. The habitat mapping included the following two components conducted at each of 30 reserves: 1) Elevation-based mapping, using NOAA-generated elevation models and tidal datums to estimate the potential extent of the estuary, and identify areas no longer subject to tidal influence that could be restored in the future, and 2) Historical mapping, using the oldest T-sheet (topographic map) or Lake Survey map to examine extent and distribution of habitats in one smaller area of interest on/near each reserve, and document how that has changed over time. The project generated various products for each of the 30 reserves: technical reports detailing findings, historical maps available as raw image files, and geodatabases in local coordinates with both elevation-based and historical mapping analyses.