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  • Title

    Habitat, hatcheries, and nonnative predators interact to affect juvenile salmon behavior and survival

    Lead University of California - Santa Cruz [UCSC]
    Description Chinook salmon are an iconic part of California’s environment and heritage, and important both economically and culturally. In the Sacramento River, the winter-run Chinook population is endangered, and there is strong interest in restoring these populations. To do so, resource managers need to better understand the pressures on wild populations. Predation by nonnative predators affects survival of young salmon but may also affect the behavior of salmon. Changes to salmon behavior also have costs but are not currently considered in management. Managers need information on how predators affect juvenile salmon behavior, how they might vary under different conditions, and how they scale up to affect populations.
    Science topics Chinook Salmon, Fishing
    Updated November 17, 2022
  • Title

    Marine Invasive Species Program [MISP]

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Marine Invasive Species Program (MISP) is responsible for analysis of shipping vectors (pathways) responsible for the introduction of non-indigenous species (NIS) into California's coastal waters. MISP has partnered with the Smithsonian Environmental Research Center (SERC) and Moss Landing Marine Laboratories (MLML) to undertake an extensive program to analyze spatial and temporal patterns of NIS invasions in marine and estuarine waters of California. MISP collaborates with the California State Lands Commission (CSLC) to regulate and minimize the introduction of Nonindigenous Species (NIS) into California by ocean-going vessels. MISP is partners with the Smithsonian Environmental Research Center (SERC) to conduct biological surveys monitoring the coastal waters of California to determine the level of invasion by NIS;and San Jose State University's Moss Landing Marine Labs (MLML) to conduct genetic analysis of NIS. The California Ballast Water Management Act of 1999 initiated baseline surveys by the California Department of Fish and Wildlife (CDFW) to document the distribution of nonindigenous species in the state's coastal and estuarine waters.
    Science topics Striped bass, Corbicula and Potamocorbula, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Invasive and non native species
    Updated April 29, 2022
  • Title

    San Francisco Bay Bathymetry

    Lead U.S. Geological Survey [USGS]
    Description USGS has conducted bathymetric analyses in San Francisco Bay, Suisun Bay, and the Delta intermittently since 1867 based on bathymetry data primarily collected by NOAA"s National Ocean Service (NOS) (formerly the United States Coast and Geodetic Survey (USCGS)). Since the days of hydraulic gold mining, sedimentation in San Francisco Bay has changed drastically. From the 1850's until at least the late 1800's, debris from hydraulic mining in the Sierra Nevada filled the Bay. As hydraulic mining practices ceased, the amount of sediment deposited decreased. In the latter half of the 20th century an increase in the implementation of flood control and water distribution projects in the Central Valley caused the Bay to be erosional due to the reduction of the frequency and duration of peak flow conditions, which in turn decreased sediment supply to the Bay. They have used this information to locate deposits of sediment-associated contaminants, restore wetland areas, and to provide the observable linkage between anthropogenic modifications of the landscape—such as evolving land use practices, flood control, and water diversions—and natural forces of climate-driven river flow, sea level change, tides, and wind. In 1999, USGS assessed how sedimentation in the Suisun Bay has changed between 1867 and 1990 (see info sources). They have also worked collaboratively with DWR, using their more recent bathymetry data to produce a high-resolution DEM of the Delta region (see info sources). It is not clear whether USGS will continue their bathymetry surveys. The latest survey is from 2005, and took place in the South of San Francisco Bay (outside the Delta study area).
    Science topics Flood, Land elevation, Bedload, Deposition, Erosion, Main channels, Sloughs, Backwater
    Updated April 29, 2022
  • Title

    AmeriFlux Network

    Lead U.S. Department of Energy - Office of Biological and Environmental Research [DOE-BER]
    Description

    AmeriFlux is a network of PI-managed sites measuring ecosystem CO2, water, and energy fluxes in North, Central and South America. AmeriFlux is now one of the DOE Office of Biological and Environmental Research (BER) best-known and most highly regarded brands in climate and ecological research. AmeriFlux datasets, and the understanding derived from them, provide crucial linkages between terrestrial ecosystem processes and climate-relevant responses at landscape, regional, and continental scales. Scientific Questions What are the magnitudes of carbon storage and the exchanges of energy, CO2 and water vapor in terrestrial systems? What is the spatial and temporal variability? How is this variability influenced by vegetation type, phenology, changes in land use, management, and disturbance history, and what is the relative effect of these factors? What is the causal link between climate and the exchanges of energy, CO2 and water vapor for major vegetation types, and how does seasonal and inter-annual climate variability and anomalies influence fluxes? What is the spatial and temporal variation of boundary layer CO2 concentrations, and how does this vary with topography, climatic zone and vegetation?
    Science topics Agriculture, Air temperature, Carbon, Delta islands, Environmental drivers, Forests, Habitat, Non forested vegetation, Precipitation, Solar irradiance, Wind
    Updated June 3, 2025
  • Title

    Anadromous Fish Distribution

    Lead California Department of Fish and Wildlife [CDFW]
    Description To meet the need for consistent statewide anadromous distribution data, CalFish cooperators have initiated a series of projects to begin pulling existing distribution data together for select anadromous species. We began developing Coho Distribution in 2002, published the first publicly available version in July 2007 and most recently updated with new information in June 2012. We extended this effort to Steelhead in the Fall of 2004, first published the data in the Fall of 2007 and updated it in Fall 2009 and most recently June 2012. Additionally, we are seeking funding to further extend this effort to Chinook in the very near future.
    Science topics Fishing, Main channels, Sloughs, Backwater, Chinook Salmon, Steelhead Trout
    Updated April 29, 2022
  • Title

    Freshwater CyanoHABs Program [Blue-Green Algae Harmful Algal Blooms]

    Lead California State Water Resources Control Board [SWRCB]
    Description Observations of harmful algal blooms (HABs) and algal toxins have increased globally in recent years. HABs are problematic because they can affect multiple beneficial uses including recreation, aquatic life, and drinking water by reducing aesthetics, lowering dissolved oxygen concentration, causing taste and odor problems, and producing potent toxins. Water Board staff are working with state and local entities to identify and respond to HAB incidents throughout California. The Water Board first began to formally address this issue in 2005 when it formed the Blue Green Algae Work Group, later renamed the California Cyanobacteria Harmful Algal Bloom Network (CCHAB). An initial product of this group was the Voluntary Guidance Document (original release 2010, updated 2016). Subsequently, SWAMP prepared California Freshwater HAB Assessment and Support Strategy to articulate a coordinated program to assess, communicate and manage HABs in California.
    Science topics Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Benthos, Saltwater and freshwater marshes, Environmental drivers, Socio economic drivers, Other species
    Updated April 29, 2022
  • Title

    Smelt Larva Survey

    Lead California State Water Resources Control Board [SWRCB]
    Description The Smelt Larva Survey provides near real-time distribution data for longfin smelt larvae in the Delta, Suisun Bay and Suisun Marsh. Sampling takes place within the first two weeks in January and repeats every other week through the second week in March. Each 4-day survey consists of a single 10-minute oblique tow conducted at each of the 35 survey locations (see map) using an egg and larva net. The 505-micron mesh net is hung on a rigid frame shaped like an inverted-U, which in turn is attached to skis to prevent it from digging into the bottom when deployed. The net mouth area measures 0.37 m2. The conical net tapers back from the frame 3.35 m to a 1-liter cod-end jar, which collects and concentrates the sample. Immediately after each tow, juvenile fishes are removed, identified, measured and returned to the water immediately, and the remaining larvae are preserved in 10% formalin for later identification in the Lab in Stockton.
    Science topics Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity
    Updated April 29, 2022
  • Title

    Spring Kodiak Trawl Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Spring Kodiak Trawl Survey (SKT) has sampled annually since its inception in 2002. The SKT determines the relative abundance and distribution of spawning delta smelt (Hypomesus transpacificus). The SKT samples 40 stations each month from January to May. These 40 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, Walnut Grove on the Sacramento River, and the Sacramento Deep Water Ship Channel. Each 'Delta-wide' survey takes approximately 4 - 5 days per month to complete. Historically, 'Delta-wide' surveys were followed by a 'Supplemental' survey two weeks later to intensively sample areas of highest delta smelt concentration to estimate the proportion of male and female delta smelt that were in pre-spawning, spawning and spent maturation stages. Beginning in 2008, in an effort to minimize take of spawning adults, routine 'Supplemental' surveys were discontinued and are now only conducted under the recommendation of the Smelt Working Group and the approval of managers.
    Science topics Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity, Other species
    Updated April 29, 2022
  • Title

    Multibeam Delta Bathymetry Surveys

    Lead California Department of Water Resource [DWR]
    Description The California Department of Water Resources (CA-DWR), North Central Region Office (NCRO), Bathymetry and Technical Support Section has conducted bathymetry surveys in the Delta since 2011 (according to the Bathymetry Catalog). Data have been used to support planning for the installation of behavioural fish barriers, to assess the river’s channel capacity and ability to convey flows, to assess water quality dynamics, to better understand the area’s risk of flooding and to improve the quality of flood hazard data and maps available to local communities (under the DWR’s FloodSAFE California Initiative), to improve knowledge of sediment presence and movement, to provide high-resolution bathymetry data for hydraulic models, to assess the placement of a drought barrier, to determine how the channel bottom is evolving due to the installation of an emergency drought barrier, and to determine the effects of fish passage projects.
    Science topics Flood, Land elevation, Main channels, Sloughs, Backwater
    Updated April 29, 2022
  • Title

    Sacramento District Water Control Data System [WCDS]

    Lead U.S. Army Corps of Engineers [USACE]
    Description The Sacramento District's Water Control Data System (WCDS) collects data necessary for the management of Corps Reservoirs and Flood Control Space in Non-Corps Reservoirs (i.e.,"Section 7" projects)
    Science topics Water operations / exports, Water storage, Water conveyance / infrastructure, Wastewater discharge, Surface water flow, Stage, Flood, Air temperature, Precipitation, Wind, Main channels, Sloughs, Environmental drivers, Snowpack and snow water equivalent SWE, Water use and demand
    Updated April 29, 2022
  • Title

    Western Regional Climate Center [WRCC] - Weather Monitoring

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description THE WESTERN REGIONAL CLIMATE CENTER (WRCC) is one of six National Oceanic and Atmospheric Administration (NOAA) Regional Climate Centers across the nation. The WRCC has been housed within DRI's Division of Atmospheric Science since its inauguration in 1986. WRCC acts as a repository for high-quality historical climate data and information for the western U.S., a region covering the eleven westernmost states, including Alaska, Hawaii, and the U.S. Affiliated Pacific Islands. WRCC offers value-added tools and maintains climate services staff to support the analysis and interpretation of climate data in support of decision-making. WRCC also helps to coordinate climate-related activities at local, state, regional, and national scales. Federal partners such as the National Integrated Drought Information System, the National Centers for Environmental Information, the Southwest Climate Adaptation Science Center, and the California Nevada Applications Program support some of WRCC's major activities. In addition to climate services, WRCC staff engage in applied research on a variety of weather and climate topics.
    Science topics Air temperature, Precipitation, Wind, Solar irradiance, Extreme heat, Extreme storms, Non forested vegetation, Evaporation and evapotranspiration
    Updated April 29, 2022
  • Title

    National Water Use Science Project [NWUSP]

    Lead U.S. Geological Survey [USGS]
    Description The USGS National Water Use Science Project (NWUSP), a component of the Water Availability and Use Science Program (WAUSP), facilitates the 5-year compilation of water use estimates for the United States as part of the National Water Census (NWC). The NWC, implemented as part of the SECURE (Science and Engineering to Comprehensively Understand and Responsibly Enhance) Water Act (Subtitle F of Public Law 111-11, the Omnibus Public Land Management Act), provides data and tools designed to support water managers in the accurate assessment of water availability at regional and national scales (https://water.usgs.gov/ watercensus/). Water managers across the United States require more complete, timely, and accurate water-availability information to support policy and decision-making, specifically, data associated with water withdrawals and consumptive use. Recognizing the limitations of current water-use data, the SECURE Water Act authorized a program that supports activities related to data collection and methods research and development at the State level. The USGS Water-Use Data and Research program (WUDR) will provide financial assistance through cooperative agreements with State water resource agencies to improve the availability, quality, compatibility, and delivery of water-use data that is collected or estimated by States. The Act requires that these State water use and availability datasets be integrated with appropriate datasets that are developed and/or maintained by the USGS.
    Science topics Surface water flow, Groundwater, Water use and demand
    Updated April 29, 2022
  • Title

    Standard Operating Procedure for Diagnosing and Addressing Predator Detections in Salmon Telemetry Data

    Lead University of Washington [UW]
    Description Tag predation is a complicating factor in juvenile salmon telemetry studies that can bias results, delay timely reporting, and prevent effective data synthesis. This project addresses the problem by (1) characterizing predatory fish movement patterns from existing telemetry data in the Delta; (2) developing a standard operating procedure for diagnosing and handling detections of predated tags in salmon telemetry studies; and (3) implementing the recommendations in a software package in Program R that includes code, a “library” of expected predator behaviors, and example vignettes. The R package will be freely available for download at www.cbr.washington.edu.
    Science topics Chinook Salmon, Endangered species, Fish, Intertidal and transition zones, Invasive and non native species, Predation, Salmon migration, Steelhead Trout, Striped bass
    Updated April 30, 2025
  • Title

    Impacts of predation and habitat on Central Valley Chinook smolt survival

    Lead University of Vermont, USGS Vermont Cooperative Fish and Wildlife Research Unit
    Description The Sacramento River in California’s Central Valley has been highly modified over the past 150 years due to mining, urbanization, and impoundment/diversion of river flow to provide water for municipal, industrial, and agricultural needs. Land use changes combined with high levels of harvest have been accompanied by drastic declines in native salmon populations, including the once abundant Chinook salmon (Oncorhynchus tshawytscha). Further, the region has been subject to the introduction and widespread establishment of non-native fish species, some of which are predators of juvenile salmon. Of the four historic ecotypes of Chinook salmon (fall, late-fall, winter, and spring runs), winter- and spring-runs have been most impacted and are currently listed as endangered and threatened respectively under the US Endangered Species act. Past research has illustrated how smoltification of juvenile salmon and outmigration from freshwater to the ocean is a time of increased mortality, and reduced survival at this life stage can impact the number of reproducing adults returning to the system in subsequent years. While these studies have provided valuable information on how habitat and environmental conditions experienced by migrating Chinook salmon smolts can affect survival, they have primarily focused on individual ecotypes during the portion of the year where downstream migrations occur. However, variation in smolt size and migration timing among ecotypes can expose migrating fish to differing environmental conditions and levels of exposure to predation, which can present distinct risks for outmigration survival. To identify the areas and environmental conditions which have the greatest relative impact on juvenile survival for each ecotype, this project will use over ten years of data (2012-2022) from acoustically tagged smolts representing all four Chinook salmon ecotypes in the Sacramento River/Central Valley. Combining these data will increase sample size relative to previous studies, the range of environmental conditions (e.g., temperature, flow, and predator abundance) modeled, the range of fish sizes, and thus, the statistical power of our analyses. We hypothesize that each ecotype will have different factors that will be the primary drivers of mortality experienced during outmigration. To test our hypotheses, we will implement Cormack-Jolly-Seber (CJS) mark-recapture models to estimate both the probability of survival through reaches of the Sacramento River delineated by acoustic receivers, and the detection probability in each reach. Survival will be modeled as a function of individual, release group, reach-specific, and time-varying covariates. Further, to examine the relative impact of predation on smolt survival, we will include an additional covariate representing predator-prey encounter rates using the Mean Free-path Length model. Finally, model selection will be applied to a series of CJS models to assess the relative impact of each covariate on smolt survival for each of the four Chinook ecotypes.
    Science topics Chinook Salmon, Environmental drivers, Fish, Flows, Habitat, Predation, Salmon migration, Water temperature
    Updated February 2, 2024
  • Title

    Monitoring Sacramento River winter-run Chinook salmon life history diversity, growth, and habitat use among varying hydroclimatic regimes

    Lead University of California - Berkeley [UC Berkeley]
    Description Sacramento River winter-run Chinook salmon have been endangered since 1994. Historically, the fish spawned during summer in cool tributaries upstream of Sacramento, but dams have limited spawning habitat to a small reach of the river. Today, survival of their offspring is heavily dependent on cool summer water releases from reservoirs, which also provide critical water supplies for irrigation, municipal, and industrial needs, as well as providing flood control and hydropower generation. During drought, this can lead to difficult management decisions. Understanding how winter run Chinook salmon respond to drought and water temperature is therefore vital to the management of this endangered population. This project tackled two outstanding questions about winter-run salmon ecology. The first was how winter-run Chinook use different rearing habitats during drought and non-drought periods, and the second was to explore which habitats provide enhanced growth during drought and non-drought periods. To answer these questions, UC Berkeley post-doc Pedro Morais used isotopic analysis of otoliths, or fish ear bones, which grow continuously throughout their lives and therefore carry a record of their environment and growth. Using otoliths, researchers can reconstruct details of fishes’ lives, including water temperature and migration patterns.
    Science topics None specified
    Updated February 1, 2024
  • Title

    Green Sturgeon Population Monitoring and Habitat Analysis

    Lead University of California - Santa Cruz [UCSC]
    Description

    The foundation of conserving a species is monitoring its abundance and habitat. This proposed work has three objectives which will help monitor green sturgeon abundance and understand green sturgeon habitat selection. These objectives build on 12 years of work to support the recovery of green sturgeon. The first objective is to continue the annual green sturgeon spawner census, while also improving our methods. This census is the main piece of information used in monitoring and assessing the Delta resident green sturgeon population. The second objective is to assess spawner site selection and habitat use which will help better understand sturgeon environmental needs so that restoration can better target those needs. The third objective is to assess the relationship between spring flow rates, temperature, and number of spawners observed, which will help managers better understand sturgeon flow cues and improve the accuracy of our spawner census.
    Science topics None specified
    Updated August 25, 2025