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  • Title

    Directed Outflow Project

    Lead U.S. Bureau of Reclamation [USBR]
    Description The U.S. Bureau of Reclamation (USBR) and California Department of Water Resources (DWR), along with collaborators, are continuing efforts to evaluate the hypothesized benefits of outflow and outflow alteration for Delta Smelt. The collective aim of these efforts is to better inform management actions that will bolster and stabilize the Delta Smelt population. The planned five-year Directed Outflow Project (DOP) seeks to assist in evaluating the overarching hypothesis that habitat quality and quantity is improved in the summer/fall when X2 is below 81 km and the LSZ occurs in Suisun Bay and Marsh, and this improvement in habitat conditions will translate into a greater catch density, health, and growth for Delta Smelt using this area
    Science topics Flows, Fish, Water management, Delta Smelt
    Updated April 29, 2022
  • Title

    Understanding the Scale and Mechanisms of Connectivity between Splittail Populations and the Implications for Management

    Lead U.S. Bureau of Reclamation [USBR]
    Description Our proposal seeks to add four elements, telemetry, genetics, physiology, and modeling, to an existing research effort on splittail. The study addresses the hypothesis that there is no difference in population dynamics between the two distinct splittail populations. To address this hypothesis we are conducting a collaborative, interdisciplinary study that includes an intensive field effort combined with state-of-the-art laboratory tools that can determine the natal origins, historical habitat use, feeding, and general health of adult splittail. With this proposal we seek to leverage additional funds that were not previously available to add the four new elements. The telemetry component will take advantage of the expansive existing array of receivers deployed in the estuary to evaluate the movements and migration of splittail. The genetic component will provide a precise means to assign individuals to their respective population, determine sex ratios, and to estimate the effective size of the populations. The physiology component will determine if the newly discovered Petaluma/Napa population of splittail exhibits different requirements and tolerances than the Central Valley population. The modeling component will apply the cumulative information gained by the overall study to evaluate the sensitivity of splittail persistence to demographic variability in population dynamics. This work will directly address the Priority Research Topics presented in the PSP.
    Science topics Sacramento Splittail
    Updated April 29, 2022
  • Title

    Aquatic Habitat Sampling Platform: Standardized Fish Community Sampling Across Habitat Types

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description The Aquatic Habitat Sampling Platform (AHSP) is an integrated aquatic species and habitat sampling system that can effectively monitor aquatic organisms and reveal habitat associations while having minimal or no “take” of sensitive species. Further development and deployment of the AHSP will expand data collection to shallow and off-channel habitat, while offering the capability to transition to deeper and open water habitats, providing reliable sampling efficiency estimates (e.g., probability fish detection) and “catch” per unit effort (i.e., number of individual species per volume of water sampled) and improving our knowledge about populations, habitat associations and major stressors of key organisms within the San Francisco Estuary (Estuary). Need Within the Estuary, numerous monitoring techniques are used. However, monitoring weaknesses for determining fish status and trends include: 1) restricted locations available for some techniques;2) limited ability to simultaneously assess zooplankton and fish larvae;and 3) difficulty in estimating fish population size due to lack of gear efficiency information (Honey et al. 2004). Furthermore, past attempts at integrated abundance indices from more than one sampling method have had limited success. Although there continues to be considerable collaborative monitoring and research devoted to understanding Central Valley fish species, coordination among activities has been difficult. Other issues include permitting take of listed species and time-consuming monitoring with extended periods of down time due to sample post-processing of fish and invertebrate species. Identification of key microhabitats for each lifestage and attributes and linking associated physical parameters such as habitat features (e.g., depth, structure, channel type) and water quality is needed. Objectives • Test AHSP operation within the Estuary while providing information highly relevant to pressing Delta management issues (IEP 2016); • Provide detailed information on distribution and approximate abundance of adult Delta Smelt within identified habitat types (Biological Opinion on the Long-Term Operational Criteria and Plan for coordination of the Central Valley Project and State Water Project;https://www.fws.gov/sfbaydelta/documents/SWPCVP_OPs_BO_12-15_final_OCR.pdf);and • Assess habitat associations and diurnal behavior of Delta Smelt and other fishes (Durand 2015).
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Central Valley Salmonid Coordinated Genetic Monitoring [Year 4]

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description This work will include tasks to rapidly identify winter-run Chinook juvenile salmon at the CVP/SWP salvage facilities, process juvenile salmonid tissues from various CVPIA and IEP fish monitoring stations, and support coordination of genetic monitoring across the CVP and SJRRP programs. PIs: Josh Israel (USBR);Scott Blankenship (Cramer Fish Science);Ken Bannister (USFWS);John Carlos Garza (NOAA-Fisheries);Brett Harvey (DWR);Noble Hendrix (QEDA);Rachel Johnson (NOAA-Fisheries);Mariah Meek (UC Davis);Kevin Reece (DWR) Need This study is needed due to the limited accuracy of Lenght at Date stock identification. Inaccurate identification of Chinook salmon is problematic because it compromises the management value of data collected from standard monitoring programs. This project will improve the science and management value of the Central Valley salmon monitoring network, supported through IEP and Central Valley Project Improvement Act (CVPIA) monitoring stations, by accurately determining stock identification of multiple Chinook salmon stocks across their distribution. Classification tables will be developed to characterize monthly and seasonal accuracy between length-at-date and genetic race assignment at IEP and BiOp monitoring locations. This multi-year dataset will be used to evaluate the likelihood of accurate assignment and potential biophysical explanatory variables influencing genetic accuracy. Objectives Improve accuracy of CVPIA and IEP monitoring programs by providing genetic stock identification information for tissues collected from Red Bluff, Knights Landing, DJFMP, salvage facilities and San Joaquin River fish monitoring stations. Samples will be collected from all four runs of Chinook salmon based on length-at-date (i.e., samples will be collected from Chinook of various sizes throughout the sampling period).
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Effect of Outflow Alteration upon Delta Smelt Habitat, Condition and Survival

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description The Directed Outflow Project (DOP) is a continuing collaborative effort among a dozen state, federal and non-governmental groups. The DOP will employ a focused spatial and temporal approach to evaluate mechanistic hypotheses directly related to the rationales provided for the summer Delta outflow action and Yolo Bypass Toe Drain action to benefit Delta Smelt, with direct relevance to the fall outflow action. Paired data collections (same location and time) of abiotic and biotic habitat constituents to test specific hypotheses will assist in avoiding prior shortcomings of using data collected for different studies/hypotheses and/or across variable spatial/temporal scales (as discussed in MAST [2015] and elsewhere). Sampling will occur during the Delta Smelt juvenile rearing-stage, a period known to be associated with the location of the low salinity zone (LSZ). Results should strengthen our understanding of the mechanisms and drivers impacting Delta Smelt vital rates and associated habitat features with a focus on outflow conditions. Results should assist in evaluating the benefit and feasibility of future flow augmentation actions for managers and decision makers. Results from this and other related studies will inform evaluations on which particular outflow-related action or group of actions provides the most benefit for Delta Smelt. Need Requests and plans for water management actions related to augmentation of Delta outflow have proceeded and are expected to proceed in the future. However, there is uncertainty and disagreement regarding the mechanistic relationship of Delta outflow during the rearing period to Delta Smelt vital rates and habitat, and the hypothesized benefit of outflow alteration for Delta Smelt. Delta outflow has experienced reductions in recent years, coinciding with the collapse of the Delta Smelt. Reduced outflow has been linked to reductions in habitat suitability in Suisun Bay and Marsh and movement of the LSZ to the Confluence of the Sacramento-San Joaquin River where little connection to shallow open water habitats exists. Objectives The DOP’s main objective will be to evaluate the hypothesized benefit of outflow alteration for Delta Smelt and its habitat in coordination with all stakeholder groups. The following process and product related sub-objectives will facilitate progression toward this evaluation objective. • Test mechanistic hypotheses addressing the rationale behind outflow-based actions to benefit Delta Smelt. • Concurrently sample fish and measure abiotic/biotic habitat conditions at each randomly selected location along the salinity and habitat gradient of the north to western Delta along the Sacramento River during the summer and fall.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Central Valley Project - Reservoir Monitoring

    Lead U.S. Bureau of Reclamation [USBR]
    Description The Central Valley Project (USBR) is responsible for maintaining and monitoring water levels in several key reservoirs in California. The reservoirs of focus (largest capacity) within the CVP are Folsom, Whiskeytown, Shasta, Trinity, San Luis, and Millerton. San Luis is jointly monitored by USBR and DWR. Reservoir storage, elevation, inflow, and outflow are monitored daily, with some parameters at certain reservoirs being monitored hourly or monthly, and reported to the California Data Exchange Center (CDEC) for public access.
    Science topics Water storage, Water conveyance / infrastructure, Surface water / flow, Stage, Flood, Precipitation, Main channels, Water use / demand, Evaporation / evapotranspiration
    Updated April 29, 2022
  • Title

    Delta-Mendota Canal Water Quality Monitoring

    Lead U.S. Bureau of Reclamation [USBR]
    Description Reclamation proposes to execute contracts with local water districts to convey non-project water in the Delta-Mendota Canal (DMC) subject to water quality monitoring, groundwater monitoring and reporting requirements outlined in this document
    Science topics Surface water / flow, Nitrogen / ammonia, Salinity, Turbidity, Hg and methyl mercury, Lead, Copper, Zinc, Arsenic, Selenium, Other discharge contaminants, Conductivity
    Updated April 29, 2022
  • Title

    Grasslands Bypass Project Monitoring

    Lead U.S. Bureau of Reclamation [USBR]
    Description The Grassland Bypass Project has been under waste discharge requirements (WDRs) since 1998. Historically, subsurface agricultural drainage water (tile drainage) and surface runoff (irrigation tail water) from the Grassland Watershed was discharged to the San Joaquin River through Salt Slough and/or Mud Slough (north). These two sloughs are tributary to the San Joaquin River and serve as the primary drainage outlets for the Grassland Watershed. With the start of the Grassland Bypass Project in 1996, all tile drainage from a 97,000 acre area known as the Grassland Drainage Area is consolidated and conveyed through San Luis Drain to Mud Slough, eliminating discharges of drainage water from the Grassland Drainage Area into Salt Slough and wetlands. Reducing selenium in wetland channels is the primary goal of the Project, as elevated concentrations of selenium have been documented to be hazardous to wildlife. The Project prevents discharge of subsurface agricultural drainage water into wildlife refuges and wetlands in central California . The drainage water is conveyed instead through a segment of the San Luis Drain to Mud Slough, a tributary of the San Joaquin River. The Project improves water quality in the wildlife refuges and wetlands, sustains the productivity of 97,000 acres of farmland, and fosters cooperation between area farmers and regulatory agencies in drainage management reduction of selenium and salt loading. The Project is operated by the Bureau of Reclamation and the San Luis & Delta-Mendota Water Authority (Authority).
    Science topics Agriculture, Surface water / flow, Water temperature, pH, Selenium, Conductivity
    Updated April 29, 2022
  • Title

    Central Valley Project

    Lead U.S. Bureau of Reclamation [USBR]
    Description The CVP is one of the largest water storage and transport systems in the world, comprised of 20 reservoirs and more than 500 miles of canals. This project provides water used to irrigate more than 3 million acres of agricultural land and has a total reservoir storage of 11,363,000 acre-feet.
    Science topics Water operations / exports, Water storage, Water conveyance / infrastructure, Surface water / flow, Stage, Flood
    Updated April 29, 2022
  • Title

    Benthic Organism Study

    Lead U.S. Bureau of Reclamation [USBR]
    Description This program operates under the Interagency Ecological Program's (IEP) Environmental Monitoring Program (EMP). "The Benthic Organism monitoring effort was started in 1975 and currently monitors 10 sites across the estuary's salinity gradient, from Suisun Bay upstream to Clifton Court Forebay and Stockton, on a monthly basis. Benthic invertebrates are collected with a PONAR grab, preserved, identified, and enumerated. In addition to mandated monthly monitoring of benthic invertebrates, we also conducted special studies of benthic invertebrates using spatial intensive sampling schemes. These special studies complement the long-running mandated monitoring and provide a more comprehensive picture of the benthic community of the Upper San Francisco Estuary." Changes in benthic fauna presence, abundance and distribution associates physical factors are measured in the estuary to evaluate the impacts of water project operations. 426 species in 10 phyla have been collected to date. Data is also used to detect introduced species. Sediment composition data also collected to document general trends at sites where benthic organisms are collected. https://emp.baydeltalive.com/projects/12727/page
    Science topics Suspended sediment, Bedload, Deposition, Erosion, Insects, Mollusks, Crustaceans
    Updated April 29, 2022
  • Title

    Telemetered Stream Gauge Stations [Surface Water Monitoring]

    Lead U.S. Bureau of Reclamation [USBR]
    Description A network of stream gauges record and telemeter river stage information. Flow measurements by field crews help calibrate and confirm calculations. Data from stream gage telemetry requires careful consideration as field conditions and equipment malfunctions can provide erroneous readings. A more accurate assessment of actual flow rates requires a review of the flow record and processing to account for actual conditions.
    Science topics Water operations / exports, Water conveyance / infrastructure, Surface water / flow, Stage, Flood, Main channels, Sloughs
    Updated April 29, 2022
  • Title

    Groundwater Monitoring

    Lead U.S. Bureau of Reclamation [USBR]
    Description The SJRRP has installed 211 groundwater monitoring wells with 48 locations measuring groundwater temperature. Most monitoring wells are manually measured weekly and results from fourteen key monitoring wells are available online. Groundwater levels in many of these wells will be measured electronically at a high frequency (hourly) and manual measurements will be made periodically to assure the quality of data recorded by the instruments. Generally weekly/monthly manual groundwater level measurements will be made, with more frequent weekly measurements made in priority wells. Several key wells will be telemetered, transmitted real-time to a central database, and posted on CDEC, with links from the SJRRP website (restoresjr.net).
    Science topics Water storage, Water conveyance / infrastructure, Levees, Groundwater, Water temperature, Conductivity, Water use / demand
    Updated April 29, 2022
  • Title

    Water Quality Monitoring

    Lead U.S. Bureau of Reclamation [USBR]
    Description Water Quality includes a program of real-time telemetry, generally with 15-minute reporting to the California Data Exchange Center. In addition, the SJRRP initiated a program of manual water quality constituent measurements. Reclamation will evaluate shallow groundwater, irrigation supply, subsurface drain system and San Joaquin River water quality for SJRRP seepage investigations.
    Science topics Chlorophyll A / B, Water temperature, Dissolved oxygen, pH, Turbidity, Insecticides, Rodenticides, Herbicides, Fungicides, Other discharge contaminants, Main channels, Sloughs, Conductivity
    Updated April 29, 2022
  • Title

    Fish Salvage and Genetic Analysis

    Lead U.S. Bureau of Reclamation [USBR]
    Description The State Water Project (SWP), operated by the California Department of Water Resources (DWR), and the Central Valley Project (CVP), operated by the U.S. Bureau of Reclamation, export water out of the San Francisco Bay Delta for urban and agricultural use in California. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Since 1957, the U.S. Bureau of Reclamation (USBR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). CDFW's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in 1968. Fish salvage and loss rates are used to determine the need for changes in operations in response to National Marine Fisheries Service (NMFS) regulatory requirements. Salvage and loss monitoring includes daily monitoring and reporting of estimated loss of salvaged fish, as well as monitoring and reporting of salvaged Coded Wired Tagged (CWT) hatchery fish. This information is widely used by West Coast fisheries agencies to collect information on natural and hatchery-reared stocks of salmon and steelhead. Our state-of-the-art genetic analysis techniques are used to quantify salvage rates of listed runs of California's Central Valley juvenile Chinook Salmon. We also utilize advanced genetic analysis techniques to identify different populations of Central Valley juvenile Chinook Salmon, and actively participate in development of new analysis methods.
    Science topics Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish, Invasive / non native species
    Updated April 29, 2022
  • Title

    Sacramento Prediction and Assessment of Salmon [SacPAS]

    Lead U.S. Bureau of Reclamation [USBR]
    Description CVPAS for Central Valley Prediction and Assessment of Salmon, extends and improves the SacPAS real-time web database and fish forecasting tools to other river systems in the Central Valley. The goal is to integrate environmental/fish data, fish passage/survival models and output from water quality models into a web-accessible analysis and visualization system. The website provides support for regional integration and public access to Reclamation and ESA-mandated activities.
    Science topics None specified
    Updated April 29, 2022
  • Title

    SAIL [Coordinated Enhanced Acoustic Telemetry Program]

    Lead U.S. Bureau of Reclamation [USBR]
    Description These monitoring efforts can provide critical information on juvenile salmonid distribution and survival, which inform biologists and managers interpretations of the exposure and intensity of CVP and SWP water operation risks on tagged populations in Central Valley rivers and the Bay- Delta. Understanding salmon survival and migration dynamics in the Delta and its tributaries is critical to the recovery of ESA-listed species, and sport and commercial fisheries management. For example, estimating the population size of endangered Sacramento River Winter-run Chinook (SRWRC) as they enter and exit the Delta is considered critical for informing Delta water management actions (Interagency Ecological Program (IEP) SAG 2013). “The use of realtime acoustic receivers that immediately transmit acoustic tagged (AT) fish detections needs to be included in the expanded network” (Johnson et al., in press). Tracking the fate of individual tagged fish will be accomplished with AT and used to develop estimates of survival and movement for other non-AT fish also part of that group. Population level sampling programs will use survival estimates generated by AT and applied to other mass marked (coded wire tagging) groups to develop improved capture efficiency for these sampling programs. Objectives: • Deploy and service field monitoring acoustic telemetry stations at locations important to fish and water management. • Implant, transport, and release acoustically tagged juvenile ESA-listed wild and hatchery juvenile salmonids. • Analysis and synthesis to support production and development of new metrics for understanding the survival, distribution, and entrainment of juvenile salmonid along the Sacramento River and its floodways, as well as, the Bay-Delta. Six-Year Steelhead Study Continuation Reclamation’s Proposed Action for ROC on LTO Section 4.10.5.12.3 Additional Measures includes a San Joaquin Basin Steelhead Telemetry Study -- Continuation of the 6-Year Steelhead telemetry study for the migration and survival of San Joaquin Origin Central Valley Steelhead. This investigation involves undertaking experiments utilizing acoustically-tagged salmonids to confirm proportional causes of mortality due to flows, exports, and other project and non-project adverse effects on steelhead smelt out-migrating from the San Joaquin Basin and through the southern Delta. This study is to coincide with different periods of operations and focus on clipped hatchery steelhead (Oncorhynchus mykiss). The period of interest is between February 15 and June 15, which coincides with a majority of O. mykiss outmigration from the Stanislaus River and recoveries of steelhead smolts in the Mossdale fish monitoring efforts. This period is to include changes in CVP/SWP operations that include reductions in exports, reductions in reverse flows in Old and Middle rivers (OMR), and San Joaquin River pulse flows to assess the influence of flow and exports on juvenile steelhead survival. This study is designed to evaluate juvenile steelhead route selection at channel divergences in the south Delta and along the mainstem San Joaquin River, and how these behaviors influence survival in specific reaches and through the Delta to Chipps Island.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Food Temperature Optimization Model for CVP

    Lead U.S. Bureau of Reclamation [USBR]
    Description This study aims to improve understanding of how nutrient and zooplankton exports from CVP reservoirs impact downstream food web productivity.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Pacific States Marine Fisheries Commission Coleman-Nimbus Tagging

    Lead U.S. Bureau of Reclamation [USBR]
    Description 25% of fall- run Chinook tagged and clipped and annual report on hathchery contributions to fisheries and watersheds
    Science topics None specified
    Updated April 29, 2022
  • Title

    Red Bluff Diversion Dam Rotary Screw Traps

    Lead U.S. Bureau of Reclamation [USBR]
    Description Annual juvenile production estimates for ESA species in Sacramento River, Clear Creek, and Battle Creek
    Science topics None specified
    Updated April 29, 2022
  • Title

    Sacramento River Basin Salmonid Monitoring with Pacific States

    Lead U.S. Bureau of Reclamation [USBR]
    Description This study aims to monitor effectiveness of salmonid habitat improvement projects in the Sacramento River basin. Annual Chinook escapement estimates in Sacramento River and upper river tributaries and American, and habitat project juvenile monitoring.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Directed Outflow Project [DOP] - Paired Habitat Sampling

    Lead U.S. Bureau of Reclamation [USBR]
    Description Special study supporting water quality, food web, and biological measures regarding seasonal outflow and Delta Smelt.
    Science topics Flows, Water management
    Updated April 29, 2022
  • Title

    FCCL Conservation Hatchery Operation for Delta Smelt Refuge Population Maintenance and Research Support

    Lead U.S. Bureau of Reclamation [USBR]
    Description This facility houses the Delta Smelt Refuge population and produces Delta Smelt for release into the Delta. It is also responsible for the genetic management of the captive population and support of studies on supplementation.
    Science topics Delta Smelt
    Updated April 29, 2022