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  • Title

    Delta Regional Monitoring Program Mercury Monitoring

    Lead Delta Regional Monitoring Program [RMP]
    Description Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest priority information needs related to implementation of the Sacramento–San Joaquin Delta Estuary Total Maximum Daily Load (TMDL) for Methylmercury (Wood et al. 2010). Two species of sport fish, largemouth bass (Micropterus salmoides) and spotted bass (Micropterus punctulatus), were collected at six sampling locations in August and September 2016. The length-adjusted (350 mm) mean methylmercury (measured as total mercury, which is a routinely used proxy for methylmercury in predator fish) concentration in bass ranged from 0.15 mg/kg or parts per million (ppm) wet weight at Little Potato Slough to 0.61 ppm at the Sacramento River at Freeport. Water samples were collected on four occasions from August 2016 through April 2017. Concentrations of methylmercury in unfiltered water ranged from 0.021 to 0.22 ng/L or parts per trillion. Concentrations of total mercury in unfiltered water ranged from 0.91 to 13 ng/L. Over 99% of the lab results for this project met the requirements of the Delta RMP Quality Assurance Program Plan, and all data were reportable. This data report presents the methods and results for the first year of monitoring. Historic data from the same or nearby monitoring stations from 1998 to 2011 are also presented to provide context. Monitoring results for both sport fish and water were generally comparable to historic observations. For the next several years, annual monitoring of sport fish will be conducted to firmly establish baseline concentrations and interannual variation in support of monitoring of long-term trends as an essential performance measure for the TMDL. Monitoring of water will solidify the linkage analysis (the quantitative relationship between methylmercury in water and methylmercury in sport fish) in the TMDL. Water monitoring will also provide data that will be useful in verifying patterns and trends predicted by numerical models of mercury transport and cycling being developed for the Delta and Yolo Bypass by the California Department of Water Resources (DWR).
    Science topics Biosentinels, Fish, Methylmercury, Restoration, Water
    Updated November 17, 2022
  • Title

    Yolo Bypass Salmonid Habitat Restoration and Fish Passage: Scenario Analysis of Fremont Weir Notch – Integration of Engineering Designs, Telemetry, and Flow Fields

    Lead U.S. Army Corps of Engineers [USACE]
    Description This study analyzes 12 notch scenarios in the Fremont Weir in terms of entrainment of juvenile salmon. The goal is to quantify the relative entrainment rates (between 0 and 1) across the suite of scenarios and to identify possible strategies for enhancing entrainment outcomes. This study does not predict future entrainment as models generally do not predict future outcomes so much as highlight trends
    Science topics Chinook Salmon, Endangered species, Water conveyance / infrastructure
    Updated April 29, 2022
  • Title

    Review of Four Juvenile Salmon Coded Wire Tag Experiements Conducted in the Delta

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The US Fish and Wildlife Service, Stockton Fish and Wildlife Office, has since the mid-1980s conducted several multi-year release-recovery experiments with coded-wire-tagged juvenile Chinook salmon. The objectives of the studies were (1) to estimate survival through the lower portions of the Sacramento and San Joaquin river systems, the California Delta, and (2) to quantify the factors affecting survival. Four of these studies, listed more or less by their historical start dates, are the Delta Cross Channel, Interior, Delta Action 8, and VAMP experiments.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Predicting the Effects of Invasive Hydrozoa [Jellyfish] on Pelagic Organisms Under Changing Salinity and Temperature Regimes

    Lead University of California - Davis [UC Davis]
    Description The purpose of this project seeks to investigate the potential effects of jellyfish, a devising invader of some ecosystems, on the SFE ecosystem, to determine the key factors allowing successful establishment and spread of these species, and to predict future effects and spread of the invasions.
    Science topics Water temperature, Salinity, Pelagic fish, Jellyfish
    Updated April 29, 2022
  • Title

    Climate change impacts to San Francisco Bay-Delta wetlands: Links to pelagic food webs and predictive responses based on landscape modeling

    Lead San Francisco State University [SFSU]
    Description The purpose of this project is to 1) evaluate the potential impacts of climate change on SF Bay-Delta tidal wetlands, 2) improve our understanding of the linkage between these wetlands and the pelagic food web, especially fish populations, and 3) use this information to make predictions about potential effects of climate change on Bay-Delta fish populations.
    Science topics Pelagic fish, Wetlands
    Updated April 29, 2022
  • Title

    Comparison of Nutrient Sources and Phytoplankton Growth and Species Composition in Two Rivers: Their Roles in Determining Productivity and Food Web Conditions in Suisun Bay and the Delta

    Lead San Francisco State University [SFSU]
    Description
    Science topics Phytoplankton, Pelagic fish, Nitrogen / ammonia
    Updated April 29, 2022
  • Title

    Biomass and Toxicity of a Newly Established Bloom of the Cyanobacteria Microcystis aeruginosa and its Potential Impact on Beneficial Use in the Sacramento-San Joaquin Delta

    Lead California Department of Water Resource [DWR]
    Description Monitoring and simple analysis of the extent of this cyanobacteria in the Delta, and preliminary exploration of the impacts of cystins on drinking water quality, and human and wildlife health.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Environmental Monitoring Program: Continuous Water Quality Monitoring

    Lead California Department of Water Resource [DWR]
    Description DWR has conducted water quality monitoring for the California State Water Project since 1968. This program is currently managed by the Division of Operations and Maintenance, Environmental Assessment Branch. Initially, this program sought to monitor eutrophication (an increase in chemical nutrients) and salinity in the SWP. Over time, the water quality program expanded to include parameters of concern for drinking water, recreation, and wildlife. DWR's Division of Operations and Maintenance (O&M) currently maintains 16 continuous water quality monitoring stations located throughout the State Water Project. Data from these automated stations are uploaded to the California Data Exchange Center (CDEC) website. Hourly to daily conductivity, temperature, turbidity, pH, fluorometry, UVA-254 absorption
    Science topics Air temperature, Algae, Chemistry, Chlorophyll A / B, Conductivity, Cyanobacteria, Dissolved oxygen, Drought, Environmental drivers, Estuaries, Harmful algal blooms HAB, Nitrogen, Nutrients, pH, Phytoplankton, Primary production, Salinity, Surface water / flow, Temperature, Tides, Turbidity, Water, Water conveyance / infrastructure, Water management, Water temperature
    Updated May 21, 2024
  • Title

    Environmental Monitoring Program (EMP)

    Lead California Department of Water Resource [DWR]
    Description

    The Environmental Monitoring Program (EMP) began in 1975 to conduct baseline and compliance monitoring of water quality, phytoplankton, zooplankton, and benthic invertebrates in the San Francisco Bay-Delta estuary. This monitoring program was designed to track the impact of water diversions to the State Water Project (SWP) and Central Valley Project (CVP) on the Bay-Delta. In the decades since, EMP scientists have monitored these constituents at fixed and floating stations throughout the estuary and ensured compliance with state and federal mandates such as Water Right Decision 1641 (D-1641). In the years and decades since its inception, EMP has become one of the cornerstones for scientists' and managers' understanding of the pace and pattern of change in this critical ecosystem. By sampling water quality and biological communities concurrently, EMP has created a dataset that is uniquely useful in better understanding causal connections between physical, biological, and biogeochemical processes. 

    Science topics Algae, Ammonia, Benthic, Benthos, Bivalve, Carbon, Chemistry, Chlorophyll A / B, Climate change, Conductivity, Corbicula/Potamocorbula, Crustaceans, Cyanobacteria, Delta islands, Detritus, Dissolved oxygen, Docks and ports, Drought, Environmental drivers, Estuaries, Food webs, Harmful algal blooms HAB, Invasive / non native species, Invertebrates, Jellyfish, Main channels, Mollusks, Nitrogen, Nitrogen / ammonia, Nutrients, Open water, Other species, Other zooplankton, pH, Phosphorous, Phytoplankton, Primary production, Salinity, Sediments, Sloughs, Surface water / flow, Suspended sediment, Temperature, Tidal wetlands, Tides, Turbidity, Water, Water conveyance / infrastructure, Water management, Water operations / exports, Water temperature, Zooplankton
    Updated October 16, 2024
  • Title

    Yolo Bypass Fish Monitoring

    Lead California Department of Water Resource [DWR]
    Description California Department of Water Resources (DWR) has operated a fisheries monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: (1) collect baseline data on lower trophic levels (phytoplankton, zooplankton, and aquatic insects), juvenile fish and adult fish, hydrology, and water quality parameters;(2) investigation of the temporal and seasonal patterns in chlorophyll-a concentrations, including whether high concentrations are exported from the Bypass during agricultural and natural flow events and the possibility of manipulating bypass flows to benefit listed species like Delta Smelt (Hypomesus transpacificus) and Chinook salmon (Oncorhynchus tshawytscha). The YBFMP operates a rotary screw trap and fyke trap, and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts.
    Science topics Chinook Salmon, Chlorophyll A / B, Conductivity, Delta Smelt, Direction, Dissolved oxygen, Endangered species, Fish, Flood, Food webs, Green sturgeon, Habitat, Habitat restoration, Insects, Intertidal / transition zones, Invasive / non native species, Invertebrates, Longfin Smelt, Main channels, Nitrogen, Nitrogen / ammonia, Nutrients, Other species, Other zooplankton, Pelagic fish, pH, Phytoplankton, Primary production, Sacramento Splittail, Salmon migration, Salmon rearing, Saltwater / freshwater marshes, SAV/FAV, Seasonally flooded, Solar irradiance, Stage, Steelhead Trout, Striped bass, Sturgeon, Submerged aquatic vegetation, Surface water / flow, Tides, Turbidity, Velocity, Water, Water temperature, Wetlands, White Sturgeon, Zooplankton
    Updated August 28, 2024
  • 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 November 18, 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

    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

    Assessing sea-level rise and flooding changes in the Sacramento/San Joaquin Delta using historical water-level records

    Lead California State University [CSU]
    Description The project aims to recover, digitize, and analyze more than 1300 station years of ‘lost-and-forgotten’ water level records collected from 1857 to 1982 in the Sacramento-San Joaquin Delta. These measurements, augmented by modern data, will improve our understanding of tidal, flood, and sea level trends in the system. By determining ‘hotspots’ of habitat and flood risk sensitivity, the results may be used to better focus future scientific and management priorities, to protect the environment, manage flood risk, and enhance community resilience to climate change
    Science topics Backwater, Climate change, Environmental drivers, Estuaries, Land elevation, Levees, Outflow, Sea level rise, Stage, Subsidence, Surface water / flow, Tides, Velocity, Vessels and shipping channels, Water, Wind
    Updated October 10, 2023
  • Title

    From Microbes to Zooplankton, What Defines a Beneficial Wetland?

    Lead San Francisco State University, Estuary & Ocean Science Center
    Description Our study will characterize species diversity at multiple levels of biological organization in the water column of restoring wetlands in the upper San Francisco Estuary and Delta (SFE), from bacteria to fishes. In doing so, we will also describe the foodweb benefits being provided to larval fishes, including longfin smelt, through additional dietary DNA analysis. We will use the species diversity we find in the water column to identify a subset of biota that are indicative of the conditions present in wetlands in different stages of restoration (early, intermediate, and mature) and identify connections between those indicators to the foodweb resources being provided to higher trophic levels. We will study 3-4 wetlands in each of 3 stages: early (unvegetated), intermediate (partially vegetated and partially channelized), and mature (fully vegetated and channelized) wetlands.
    Science topics Crustaceans, Cyanobacteria, Estuaries, Fish, Food webs, Habitat, Habitat restoration, Insects, Invertebrates, Longfin Smelt, Other species, Other zooplankton, Pelagic fish, Phytoplankton, Predation, Restoration, Salinity, Saltwater / freshwater marshes, Tidal wetlands, Wetlands, Zooplankton
    Updated January 31, 2024
  • 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

    Large and small-scale sediment dynamics during (after) the drought

    Lead Delta Stewardship Council - Delta Science Program
    Description Turbidity plays a key role in Delta aquatic ecosystems, where suspended sediment can limit light for phytoplankton growth, transport contaminants, provide protection from predation for many fish species, and contribute to natural sediment recovery in shallow water habitats. The impact of drought conditions on water quality and ecological health is not well studied in estuarine systems, and more information is needed to manage the impacts of California’s drought and recovery in the Delta. This project will examine the effects of drought conditions on turbidity, particularly the interplay between estuarine turbulence, suspended sediment flocculation (particle aggregation), and in-water light levels. Information from this project will contribute fundamental knowledge on flocculation dynamics, help identify critical points for turbidity control during drought, and improve modeling and predictions of sediment transport within the Delta.
    Science topics None specified
    Updated January 4, 2024
  • Title

    Continuous Flow and Water Quality Monitoring Network in the Sacramento-San Joaquin Delta

    Lead U.S. Geological Survey [USGS]
    Description This project envisions the continuation, expansion, and further integration of high frequency monitoring for flow, water quality (including chlorophyll and nutrients), sediment, as well as biological responses at key locations in the Delta and Suisun Bay. The physical properties monitored by the fixed-station network are the primary drivers of the habitat conditions and biological responses that management actions hope to achieve. Nutrient dynamics are explicitly measured at select stations to improve our understanding of how physical dynamics, water quality and landscape features shape the base of Delta food webs. These data will provide information about drivers linked to food quantity and quality as well as potential toxins production by harmful algae. Suspended-sediment monitoring provides an understanding of the inputs and internal exchanges between regions, locations of sources and sinks, and provides insight into the underlying cause of turbidity variability in the study area. Suspended-sediment measurements gage the availability of suspended sediment for existing marshes and for proposed large-scale marsh restoration efforts in the Delta. There are a total of 5 sub-tasks in this project: • Task 1: Hydrodynamics Team – Fixed Station Network Operation and Maintenance • Task 2: BioGeoChemistry Team -- Fixed Station Network Operation and Maintenance • Task 3: Delta Sediment Team – Fixed Station Network Operation and Maintenance • Task 4: Bay Sediment Team – Fixed Station Network Operation and Maintenance • Task 5: Project Management
    Science topics Chlorophyll A / B, Conductivity, Dissolved oxygen, Flows, Nutrients, pH, Phytoplankton, Sediments, Stage, Surface water / flow, Tides, Turbidity, Velocity, Water operations / exports, Water temperature
    Updated October 21, 2024
  • Title

    Carbon Biogeochemical Cycling in Tidal Wetlands: Exploring Lateral Carbon Exchange and Sequestration Potential

    Lead University of California - Berkeley [UC Berkeley]
    Description Tidal wetlands, at the interface of land and ocean, play a critical role in carbon biogeochemical cycling and have the potential to provide major feedback to the Earth system through greenhouse gas exchange and long-term carbon sequestration. However, the efficiency of carbon sequestration in tidal systems relies on both vertical carbon exchange with the atmosphere and lateral tidal exchange with adjacent water bodies. Unfortunately, the importance of hydrologic carbon fluxes has been largely overlooked, leaving a crucial aspect of coastal wetland net carbon balance unaddressed. We employed an integrated approach to quantify vertical and lateral carbon exchange and studied their dynamics, combining eddy covariance flux measurements with on-site water quality and tidal discharge measurements, as well as manual 24h surface water samplings. Our measurements were conducted in a recently restored tidal freshwater marsh in the Sacramento-San Joaquin Delta, CA, that stands out in global networks like FLUXNET and Ameriflux owing to its impressive net ecosystem exchange of -850 g C m-2 yr-1. Using wavelet decomposition, we examined the variability of carbon exchange (CO2 and CH4) across different timescales. Through information theory and mutual information analysis, we assessed the factors influencing both vertical and lateral exchanges. Our preliminary findings suggest that variability in carbon exchange is largest at the diel scale, with plant gross primary productivity and tidal fluctuations in depth having the most significant interactions with CO2 and CH4 fluxes, respectively. Furthermore, our tidal cycle samplings revealed that dissolved inorganic carbon dominates the fraction of lateral carbon loss, accounting for approximately 80% of the export. Remarkably, similarities existed between the values for net lateral carbon export and ecosystem respiration, signifying that the dissolved, terrestrial-to-ocean carbon flux could represent one of the primary fates of the fixed carbon in this tidal ecosystem. These large dissolved inorganic carbon fluxes and their chemical speciation, are important to consider when estimating the climate mitigation potential of restored tidal wetlands.
    Science topics Carbon, Carbon storage, Greenhouse gas GHG
    Updated January 30, 2024
  • Title

    Revealing the invisible contributors to the diets of larval longfin smelt and striped bass in the San Francisco Estuary.

    Lead San Francisco State University [SFSU]
    Description To better understand why the longfn smelt is threatened, the project compared the diet of larval longfn smelt to a thriving fsh with overlapping natal habitat and of similar size and morphology— the Pacifc herring. Using new genetic analysis methods, the project aimed to elucidate species composition of fsh diets in greater detail than has been done before and to measure diferences in composition and frequency of prey across habitats. In particular, the project aimed to identify prey items that were not previously seen using traditional diet analysis methods and assess whether any prey are indicative of natal habitats
    Science topics Fish, Longfin Smelt
    Updated February 26, 2024