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27 results for “Sacramento - San Joaquin Delta”
CVPIA Predation Contact Point Study - 2021: Impacts of Water Diversions in the Sacramento – San Joaquin Delta
The Central Valley Project Improvement Act (CVPIA) has led to the implementation of a Decision Support Model (DSM) to assist in the prioritization of CVPIA restoration actions. The fall-run Chinook salmon (Oncorhynchus tshawytscha) DSM depends on a coarse-resolution salmon life-cycle model to predict the population benefits of different restoration actions and scenarios. One critical element of the life-cycle model is how to incorporate predation mortality during the juvenile rearing and outmigration portion of the salmon life-cycle in the Sacramento-San Joaquin Delta (the Delta). Of particular importance to potential restoration activities, is the predation mortality that occurs in proximity to, and as a result of contact points between predator and prey fishes. Water diversions that support agricultural and municipal use result in fish mortality through entrainment and impingement. Additionally, this infrastructure may attract both predators and prey fishes, thereby increasing predation rates and prey mortality near these anthropogenic contact points. Throughout the spring of 2021, we used ARIS (adaptive resolution imaging sonar; Sound Metrics) sonars to compare piscivore abundance at 30 small water diversions in the north Delta to adjacent shorelines. We used predation event recorders (PERs) to assess the predation risk of juvenile salmonids with linear distance (m) from diversions and other predation drivers in the north Delta. Finally, we used a boat electrofishing survey to determine the piscivore community structure and compare spatial trends in black bass (Micropterus spp.) CPUE and relative abundance throughout these waterways. Piscivore abundance was greater near small water diversions than at adjacent shorelines and the predation risk of juvenile salmonids increased with proximity to diversions. Additionally, predation risk increased with increasing piscivore abundance and decreasing water depth. The north Delta predator community was dominated by black b
CVPIA Predation Contact Point Study - 2019: Impacts of Artificial Light At Night in the Sacramento – San Joaquin Delta
The Central Valley Project Improvement Act (CVPIA) has led to the implementation of a Decision Support Model (DSM) to assist in the prioritization of CVPIA restoration actions. The fall-run Chinook salmon DSM depends on a coarse-resolution salmon life-cycle model to predict the population benefits of different restoration actions and scenarios. One critical element of the life-cycle model is how to incorporate predation mortality during the juvenile rearing and outmigration portion of the salmon life-cycle in the Sacramento-San Joaquin Delta. Of particular importance to potential restoration activities, is the predation mortality that occurs in proximity to, and as a result of contact points between predator and prey fishes. A recent Literature review and meta-analysis of potential contact points in the Sacramento-San Joaquin Delta identified artificial lighting at night (ALAN) and submerged aquatic vegetation (SAV) as two contact points that have been found to influence predation elsewhere and warrant further study in this river delta (Lehman et al. 2019). Other contact points identified in this review that may affect predation of fall-run Chinook salmon juveniles included water diversions, docks, piers, scour holes, and rip rap; however, the literature on predator prey interactions associated with these contact points is lacking (Lehman et al. 2019). These datasets cover two different experiments in the Sacramento-San Joaquin Delta during spring 2019 from April - June. One experiment focused on artificial illumination and was a paired control impact study where new artificial illumination sources were introduced into the ecosystem. The other experiment relied on existing physical contact points (SAV, docks, pilings, bridges, and diversions) and assessed predation risk as a function of proximity to these points. Both experiments used predation event recorders to quantify relative predation risk and the ALAN experiment used Adaptive Resolution Imaging Sonar (ARIS) t
Efficacy and fate of fluridone applications for control of invasive submersed aquatic vegetation in the estuarine environment of the Sacramento-San Joaquin Delta
We conducted a study in the Sacramento-San Joaquin Delta to determine efficacy of the widely used herbicide fluridone in an estuarine ecosystem. The primary goal of SAV removal was restoration of open water habitat for endangered Hypomesus transpacificus (Delta Smelt). Over 18 months and multiple sets of multi-week fluridone applications, we monitored concentrations of fluridone and responses by SAV across pairs of treated and reference sites. Fluridone concentrations in the water were generally below the 2-5 parts per billion required for SAV control. Monitoring demonstrated these low water concentrations were likely due to dissipation by tides, despite use of pelleted fluridone formulations marketed for flowing water environments. Fluridone did, however, accumulate in sediment at concentrations hundreds of times higher than those measured in the water. Nonetheless, we did not observe lasting reductions in SAV abundance or changes in SAV community composition. By demonstrating lack of efficacy of one of the few herbicides permitted for use in this estuary, this study highlights the need for development of SAV management tools tailored to the challenges of hydrologically complex environments like estuaries.
Environmental and biological data associated with captive-reared Delta Smelt Study, Sacramento-San Joaquin Delta, CA, January-March 2019
The endangered Delta Smelt Hypomesus transpacificus is an osmerid fish endemic to the upper San Francisco Estuary. A captive breeding program for the species led by the Fish Culture and Conservation Laboratory (FCCL), University of California, Davis, began in 1996 to create a refuge population. In order to better understand how captive Delta Smelt would fare in conditions outside of the hatchery, we placed captive-reared fish in enclosures in the Sacramento San-Joaquin Delta, and evaluated their ability to survive, feed, and maintain condition. Fish were acclimated in the hatchery at FCCL, tagged, swabbed, weighed, measured, and transferred to enclosures in the field. There were three types of enclosures (n=2 for each type), varying in mesh size and wrap condition. In January 2019, 384 adult Delta Smelt (243 days post hatch) were transferred to enclosures in Rio Vista. In February 2019, 360 adult Delta Smelt (278 days post hatch) were transferred to enclosures in the Deepwater Shipping Channel. For each deployment, fish remained in enclosures for approximately one month, then were retrieved from enclosures, euthanized, identified, weighed and measured. A subset were also analyzed for diet contents. During the one-month long deployments, cages were checked for biofouling, damage, and dead fish, and water quality measurements and zooplankton samples were collected.
Harmful algal bloom and aquatic weeds data from the Sacramento-San Joaquin Delta, collected to evaluate the impact of the 2021 Temporary Urgency Change Order and Emergency Drought Barrier
Condition 8 of the June 2021 Temporary Urgency Change Order for the Central Valley Project (CVP) and State Water Project (SWP) requires a special study of harmful algal blooms (HABs) in the Sacramento–San Joaquin Delta (Delta) and the spread of submersed aquatic vegetation (SAV), and floating aquatic vegetation (FAV), also referred to as “aquatic weeds”. A report on the study was submitted to the State Water Resources Control Board on June 1, 2022. This data package contains all publicly available data used in the report, including visual cyanobacteria reports, cyanotoxin data, water quality, nutrients, flow/hydrodynamics, chlorophyll-a concentrations, temperature, coverage of SAV and FAV, use of herbicides, and human populations. Many of these data were derived from other datasets, though some were collected specifically for this study
Discrete water temperature, flow, solar radiation, chlorophyll-a and inundation, Sacramento-San Joaquin Delta, CA, 1999-2019
The objective of our study is to better understand the factors affecting chlorophyll-a production within a floodplain and its transport downstream to determine how lateral connectivity influences longitudinal connectivity. The Yolo Bypass is an engineered floodplain of the Sacramento River that inundates during periods of high outflow via overtopping weirs. Water traveling through the Yolo Bypass flows parallel to the Sacramento River and re-connects to the mainstem at the southern extent of the floodplain. Several monitoring programs in the Sacramento San-Joaquin Delta and Yolo Bypass collect discrete and continuous water quality data, including chlorophyll measurements. For this study, we synthesized available flow, water temperature, chlorophyll and inundation data between March 1999 to December 2019 and modeled the effects of environmental variables and inundation on chlorophyll-a production in the floodplain, the mainstem, and downstream of the floodplain/mainstem.
Sacramento-San Joaquin Bay-Delta Continuous (15 minute) Water Quality Monitoring: South Delta Region, collected by the North Central Region Office, DWR, 1999 – ongoing
The Department of Water Resources (DWR) Water Quality Evaluation Section (WQES) provides technical expertise and program support for regulatory compliance, water operations, emergency response, and environmental restoration. Wireless telemetry is used to transmit real-time provisional data to the California Data Exchange Center (CDEC), making the data publicly available. The published dataset is quality controlled and quality assured providing detailed information at 15-minute intervals from 18 monitoring stations, using Xylem’s YSI EXO2 and YSI 6600 multiparameter sondes to document individual water quality measurements of multiple water quality parameters. The dataset informs operations for the California State Water Project and supports water quality monitoring required by Water Right Decision D-1641, the Delta Compliance Program, the South Delta Temporary Barriers and the South Delta Improvement Program. It is important to note that the start dates and subsequent equipment upgrades vary between stations and equipment leading to discrepancies in the dataset’s date ranges.
Six decades (1959-2022) of water quality in the upper San Francisco Estuary: an integrated database of 16 discrete monitoring surveys in the Sacramento San Joaquin Delta, Suisun Bay, Suisun Marsh, and San Francisco Bay
The upper San Francisco Estuary (SFE) is simultaneously a central hub of water delivery in California and home to commercially important and endangered fishes, such as Chinook Salmon, Green Sturgeon, and Delta and Longfin Smelt. Extensive ecological monitoring has been conducted for over 50 years, mainly under the auspices of the Interagency Ecological Program for the San Francisco Estuary (https://iep.ca.gov/). We integrated water quality data from 16 boat-based long-term monitoring surveys in the upper SFE. This integrated dataset includes measurements of temperature (surface and bottom), conductivity (surface), salinity (surface), Secchi depth, qualitative concentration of the toxic alga Microcystis (surface), Chlorophyll-a concentration (surface), nutrients (surface), and other parameters from 1959 - 2022. The component surveys range in sampling frequency from thrice weekly to monthly and range in duration from 5 – 60 years. Most component surveys sample at fixed stations, but the Enhanced Delta Smelt Monitoring survey uses random sites and some stations (with “EZ” in the station name) of the Environmental Monitoring Program follow the salinity field. It is highly recommended to inspect the documentation of the component surveys for more information on their methods.
Multiple-benefit Conservation in Practice: Metrics Data for Quantifying Multidimensional Impacts of Landscape Change in California's Sacramento–San Joaquin Delta
<p><strong>SUMMARY</strong><br> These data represent estimated mean value, standard error, and units for a range of metrics by land cover class in the Sacramento-San Joaquin Delta. Metrics are grouped into three major categories: Agricultural Livelihoods (including metrics for gross production value, number of agricultural jobs, and annual wages per employee), Water Quality (in terms of the application rates for pesticides identified as critical pesticides, groundwater contaminants, and those posing a high or moderate risk to aquatic organisms), and Climate Change Resilience (qualitative scores representing relative tolerance for heat, drought, and flood).</p> <p><strong>DESCRIPTION</strong><br> These data were developed to facilitate projecting the net impacts of land cover change scenarios on multiple metrics of interest to the Sacramento-San Joaquin Delta, including potential benefits and trade-offs. They were used in initial analyses of scenarios representing habitat restoration and perennial crop expansion, and they are required for using the R package "DeltaMultipleBenefits", which provides the code and work flow for repeating the initial analyses or analyzing new scenarios.</p> <p>For additional details about the development and applications of these data, please see: </p> <ul> <li>Dybala KE, et al. (In review) Multiple-benefit Conservation in Practice: A Framework for Quantifying Multi-dimensional Impacts of Landscape Change in California’s Sacramento–San Joaquin Delta </li> <li>Dybala KE (2023) <em>DeltaMultipleBenefits: Projecting the Multiple Benefits of Land Cover Change in the Sacramento-San Joaquin River Delta.</em> R package version 1.0.0. doi: 10.5281/zenodo.7718620. Available from: https://pointblue.github.io/DeltaMultipleBenefits </li> </ul> <p><strong>FUNDING STATEMENT</strong><br> These data were developed as part of the project "Trade-offs and Co-benefits of Landscape Change on Bird Communities and Ecosystem Services in the Sacramento–San Joaquin River Delta", funded by Proposition 1 Delta Water Quality and Ecosystem Restoration Program, Grant Agreement Number – Q1996022, administered by the California Department of Fish and Wildlife.</p> <p><strong>POINT OF CONTACT</strong><br> Kristen Dybala, Point Blue Conservation Science, kdybala@pointblue.org</p> <p><strong>SUGGESTED CITATION</strong><br> Dybala KE. 2023. Multiple-benefit Conservation in Practice: Metrics Data for Quantifying Multi-dimensional Impacts of Landscape Change in California’s Sacramento–San Joaquin Delta. doi:10.5281/zenodo.7504874.</p> <p><strong>DATA DISTRIBUTION</strong><br> Zenodo (https://doi.org/10.5281/zenodo.7504874)</p> <p><strong>PROGRESS</strong><br> Complete, but note that the accompanying manuscript has not yet undergone peer-review, and thus these data may require future revision.</p> <p><strong>UPDATE FREQUENCY</strong><br> As Needed</p> <p><strong>DATE</strong><br> These data were compiled in 2022, based on data from the Quarterly Census of Employment and Wages 2014-2020 (EDD 2022), annual County Agricultural Commissioners Reports 2014-2020 (CDFA 2022), Pesticide Use Report Data 2014-2018 (CDPR 2022), and qualitative assessments of climate change resilience (Peterson et al. 2020, DSC 2021).</p> <p><strong>Literature Cited:</strong></p> <ul> <li>CDFA. 2022. County Ag Commissioners’ Data Listing. California Department of Food & Agriculture. Available from: https://www.nass.usda.gov/Statistics_by_State/California/Publications/AgComm/index.php</li> <li>CDPR. 2022. Pesticide Use Report Data. California Department of Pesticide Regulation. Available from: https://www.cdpr.ca.gov/docs/pur/purmain.htm</li> <li>DSC. 2021. Delta Adapts: Creating a Climate Resilient Future. Public Review Draft. Delta Stewardship Council. Available from https://deltacouncil.ca.gov/delta-plan/climate-change</li> <li>EDD. 2022. Quarterly Census of Employment and Wages (QCEW). California Employment Development Department. Available from: https://data.edd.ca.gov/Industry-Information-/Quarterly-Census-of-Employment-and-Wages-QCEW-/fisq-v939</li> <li>Peterson C, Marvinney E, Dybala K. 2020. Multiple Benefits from Agricultural and Natural Land Covers in the Central Valley, CA. Migratory Bird Conservation Partnership, Sacramento, CA. Dryad Dataset doi:10.25338/B8061X</li> </ul> <p><strong>FIELD DEFINITIONS</strong></p> <ul> <li><strong>METRIC_CATEGORY: </strong>Broad grouping assigned to each METRIC; one of Agricultural Livelihoods, Water Quality, or Climate Change Resilience</li> <li><strong>METRIC: </strong>Specific metric being estimated; one of Agricultural Jobs, Annual Wages, Gross Production Value, Drought, Flood, Heat, Critical Pesticides, Groundwater Contaminant, or Risk to Aquatic Organisms</li> <li><strong>UNIT: </strong>The units in which the <strong>METRIC </strong>is estimated</li> <li><strong>CODE_NAME:</strong> The land cover class or subclass for which the <strong>METRIC </strong>is estimated</li> <li><strong>LABEL: </strong>A more user-friendly version of <strong>CODE_NAME</strong>, useful for creating figures and tables</li> <li><strong>SCORE_MEAN:</strong> The mean value of each METRIC estimated for each land cover class or subclass</li> <li><strong>SCORE_SE: </strong>The standard error of the mean</li> </ul> <p><strong>ABBREVIATION DEFINITIONS</strong></p> <ul> <li><strong>FTE: </strong>full-time equivalents; refers to converting monthly agricultural jobs data to annual estimates by dividing by 12</li> <li><strong>ha:</strong> hectares</li> <li><strong>kg: </strong>kilograms</li> <li><strong>USD: </strong>U.S. dollars</li> <li><strong>yr: </strong>year</li> </ul> <p><strong>ACCESS & USE CONSTRAINTS</strong><br> CC-by-4.0 (https://creativecommons.org/licenses/by/4.0/)</p> <p><strong>KEYWORDS</strong></p> <ul> <li><strong>Themes:</strong> agriculture, livelihoods, economy, water quality, pesticides, climate change, resilience, multiple-benefit conservation</li> <li><strong>Place:</strong> Sacramento-San Joaquin River Delta, Central Valley, California<br> </li> </ul>
Multiple-benefit Conservation in Practice: Supplemental Spatial Data for Quantifying Multidimensional Impacts of Landscape Change in California's Sacramento–San Joaquin Delta
<p><strong>SUMMARY</strong><br> Spatial data representing climate, proximity to streams, and probability of flooding in the Sacramento-San Joaquin Delta.</p> <p><strong>DESCRIPTION</strong><br> These data were compiled as predictors of the distribution of riparian landbird species and groups of waterbird species, to facilitate projecting the probability of species or group presence across a given landscape. They were used to identify Priority Bird Conservation Areas and in analyses of the impacts of scenarios representing habitat restoration and perennial crop expansion on suitable habitat. These data are required for using the R package "DeltaMultipleBenefits", which provides the code and work flow for repeating the initial analyses or analyzing new scenarios.</p> <p>For additional details about the development and applications of these data, please see: </p> <ul> <li>Dybala KE, et al. (<em>In review</em>) Multiple-benefit Conservation in Practice: A Framework for Quantifying Multi-dimensional Impacts of Landscape Change in California’s Sacramento–San Joaquin Delta</li> <li>Dybala KE, Sesser K, Reiter M, Shuford WD, Golet GH, Hickey C, Gardali T (<em>In review</em>) Priority Bird Conservation Areas in California’s Sacramento–San Joaquin Delta. </li> <li>Dybala KE (2023) <em>DeltaMultipleBenefits: Projecting the Multiple Benefits of Land Cover Change in the Sacramento-San Joaquin River Delta</em>. R package version 1.0.0. doi: 10.5281/zenodo.7718620. Available from: https://pointblue.github.io/DeltaMultipleBenefits.</li> </ul> <p><strong>FUNDING STATEMENT</strong><br> These data were developed as part of the project "Trade-offs and Co-benefits of Landscape Change on Bird Communities and Ecosystem Services in the Sacramento–San Joaquin River Delta", funded by Proposition 1 Delta Water Quality and Ecosystem Restoration Program, Grant Agreement Number – Q1996022, administered by the California Department of Fish and Wildlife.</p> <p><strong>POINT OF CONTACT</strong><br> Kristen Dybala, Point Blue Conservation Science, kdybala@pointblue.org</p> <p><strong>SUGGESTED CITATION</strong><br> Dybala KE. 2023. Multiple-benefit Conservation in Practice: Supplemental Spatial Data for Quantifying Multidimensional Impacts of Landscape Change in California’s Sacramento–San Joaquin Delta. doi:10.5281/zenodo.7672193.</p> <p><strong>DATA DISTRIBUTION</strong><br> Zenodo (https://doi.org/10.5281/zenodo.7672193)</p> <p><strong>PROGRESS</strong><br> Complete</p> <p><strong>UPDATE FREQUENCY</strong><br> None planned</p> <p><strong>DATE</strong><br> These data were compiled in 2022, based on data from WorldClim (representing 1970-2000), National Hydrography Dataset (published 2020), and Point Blue's Water Tracker (representing 2013-2019).</p> <p><strong>FIELD DEFINITIONS</strong></p> <ul> <li><strong>bio_1: </strong>annual mean temperature (C), 1970-2000 (WorldClim; Fick and Hijmans 2017)</li> <li><strong>bio_12:</strong> total annual precipitation (mm), 1970-2000 (WorldClim; Fick and Hijmans 2017)</li> <li><strong>streamdist: </strong>square root of the distance to the nearest stream (m) (National Hydrography Dataset; USGS 2020)</li> <li><strong>pwater_fall:</strong> mean probability of open surface water during the fall, 2013-2019 (Point Blue Water Tracker; Reiter et al. 2018)</li> <li><strong>pwater_win:</strong> mean probability of open surface water during the winter, 2013-2019 (Point Blue Water Tracker; Reiter et al. 2018)</li> </ul> <p><strong>Literature Cited</strong></p> <ul> <li>Fick SE, Hijmans RJ. 2017. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int J Climatol. 37:4302–4315. <a href="https://doi.org/10.1002/joc.5086">https://doi.org/10.1002/joc.5086</a> </li> <li>Reiter ME, Elliott NK, Barbaree B, Moody D. 2018. An automated open surface water tracking system for California’s Central Valley. Report to the U.S. Fish and Wildlife Service. Petaluma, California: Point Blue Conservation Science. Available from: <a href="https://data.pointblue.org/apps/autowater/ ">https://data.pointblue.org/apps/autowater/ </a></li> <li>[USGS] United States Geological Survey. 2020. National Hydrography Dataset Best Resolution (NHD) for Hydrologic Units (HU) 4 - 1802, 1803, 1804, 1805. Reston (VA): U.S. Geological Survey. Available from: <a href="https://www.usgs.gov/core-science-systems/ngp/national-hydrography/access-national-hydrography-products ">https://www.usgs.gov/core-science-systems/ngp/national-hydrography/access-national-hydrography-products </a></li> </ul> <p><strong>ABBREVIATION DEFINITIONS</strong><br> N/A</p> <p><strong>COORDINATE REFERENCE SYSTEM</strong><br> WGS 84 / UTM zone 10N (EPSG:32610)</p> <p><strong>ACCESS & USE CONSTRAINTS</strong><br> CC-by-4.0 (https://creativecommons.org/licenses/by/4.0/)</p> <p><strong>KEYWORDS</strong></p> <ul> <li><strong>Themes:</strong> climate, temperature, precipitation, hydrology, streams, water, flood, remote sensing </li> <li><strong>Place: </strong>Sacramento-San Joaquin River Delta, Central Valley, California</li> </ul>
Interagency Ecological Program: Benthic invertebrate monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 1975-2024.
The Interagency Ecological Program’s (IEP) Environmental Monitoring Program (EMP) was initiated in compliance with the Water Right Decision D-1379 (now mandated by Water Right Decision D-1641) and has monitored benthic invertebrate macrofauna in the upper San Francisco Estuary (SFE) since 1975. The objectives of the EMP are to obtain consistent and accurate monthly data at established monitoring stations and to report this information for the purpose of management and conservation of the upper San Francisco Estuary. While the EMP also collects discrete and continuous water quality data, along with phytoplankton and zooplankton data, this dataset only includes the benthic invertebrate data collected by the EMP from 1975-2024. EMP monitors invertebrate communities in the benthos of the SFE by collecting dredge samples with a Ponar sampler. Sediment and particles smaller than 0.5mm are removed from the sample using a sieve table. The invertebrates present are preserved in formalin, identified to the lowest possible taxonomic level, and enumerated. Currently, samples are collected monthly at 10 sites across the range of salinities found in the SFE. Four replicate dredge samples are collected at each site. The frequency of sampling, number and identity of sampling sites, and number of replicate samples has changed through the 45+ years of monitoring effort, in response to changes in perceived need for data. Links to other EMP datasets can be found on the EMP website: https://emp-des.github.io/emp-reports/data-links.html, or can be found on EDI for searching for "Environmental Monitoring Program" and "San Francisco".
Hydrodynamic modeling data for Synthesis of Juvenile Steelhead Responses to Hydrodynamic Conditions in the Sacramento-San Joaquin Delta
This data release includes the output variables extracted from the UnTRIM Bay-Delta hydrodynamic model (hydrodynamic model) for use in evaluating the effects of hydrodynamics on the behavior of acoustically-tagged juvenile steelhead in the Sacramento-San Joaquin Delta. Work was funded by Proposition 1 and completed by Anchor QEA, LLC, and U.S. Geological Survey for the State Water Contractors under a Proposition 1 Grant (Evaluating Juvenile Salmonid Behavioral Responses to Hydrodynamic Conditions in the Sacramento-San Joaquin Delta), contracted by Delta Stewardship Council. Not all the hydrodynamic model output variables in the output provided with this memorandum were used in the final fish models used to analyze steelhead responses. Model output for additional variables and locations were included for completeness and to make these output files more broadly useful to researchers interested in other locations or variables in the Sacramento-San Joaquin Delta. Hydrodynamic model simulations were conducted for 2011, 2012, 2013, 2014, 2015, and 2016, with hydrodynamic model output variables provided at the same locations for each period simulated. The model simulation for each year spanned the full period of steelhead detections in the telemetry data collected during that year.
Submersed Aquatic Vegetation community multi-year data from the Sacramento - San Joaquin Delta in California
Since 2007, field data have been collected in the Sacramento - San Joaquin Delta in northern California for the purpose of training and validating invasive species maps derived from remote sensing imagery over the Delta. The field crew collected submersed aquatic vegetation (SAV) species location data. For each point they noted attributes such as species name(s), location, cover estimates, and patch size. In addition, a thatching rake tethered to a rope was thrown off the side of the boat and pulled back out of the water; Secchi depth was measured using a Secchi disk and depth to the SAV mat was estimated by the field crew. Points were collected in patches larger than 9 square meters (3 m x 3 m). Point locations were measured using high precision (sub-meter accuracy) Trimble DGPS units (Trimble Navigation Limited, Sunnyvale, California) with Wide Area Augmentation System (WAAS) differential correction. All data points were exported as ArcGIS shapefiles and projected to UTM Zone 10N, Datum WGS-84 however this dataset includes the Latitude and Longitude of each point in decimal degrees. The spatial and attribute data quality was checked by examining photos of the data points and confirming the identify of the documented species.
Sacramento-San Joaquin Bay-Delta Continuous (15 Minute) water quality monitoring data collected by the Continuous Environmental Monitoring Program, DWR, 2005- ongoing.
The Continuous Environmental Monitoring Program (CEMP) plays an instrumental role in overseeing real-time water quality in the Sacramento-San Joaquin Delta (the Delta) and Suisun Bay. The program harnesses wireless telemetry to transmit crucial data to the California Data Exchange Center (CDEC), making high-resolution environmental data pertaining to the Delta and Suisun Bay publicly accessible. The extensive dataset captures information at 15-minute intervals from 15 monitoring stations, utilizing YSI 6600 and YSI EXO sondes to obtain standalone water quality measurements. This extensive dataset informs the operations of the California State Water Project, ensuring it adheres to mandated water quality standards set by Water Right Decision 1641. This data compilation incorporates all information since the transition to YSI multiparameter sondes in 2005. It is important to note that the commencement dates and subsequent upgrades vary between stations, leading to slight discrepancies in the dataset's date ranges. Since its inception in the mid-1980s, CEMP has progressively expanded its monitoring capabilities, consistently augmenting the number of monitoring locations and the array of water quality parameters assessed. Its commitment to utilizing the most advanced water quality monitoring technology reaffirms its position as an environmental monitoring leader in the Delta and Suisun Bay. Today, the program oversees 15 water quality stations that reliably capture data every 15 minutes, each day of the year, transmitting this data in real-time. The core tenents of CEMP: • to obtain consistent and accurate data in real-time at established monitoring stations • to provide data necessary to achieve compliance with salinity, flow, and dissolved oxygen standards • to perform data analyses for further understanding of estuarine ecology • to report information to other government agencies, as well as the public, for the purpose of management and conservation of the upper San F
Submersed aquatic vegetation community composition in the Sacramento-San Joaquin Delta integrated across four surveys
Submersed aquatic vegetation (SAV) has become widespread in the Sacramento-San Joaquin Delta (Delta), and the diverse SAV assemblage is dominated by non-native species. SAV negatively impacts this estuarine ecosystem by impeding flows needed for water delivery and flood control, degrading habitat needed by native species, increasing breeding habitat for disease-vectoring mosquitoes, harboring non-native predatory fish, and hindering water recreation. The goal of this published integrated dataset is to facilitate study of these impacts. This data set includes four surveys conducted in the region during 2008-2021. Two of these are short-term special studies that have been completed, and two are ongoing long-term annual surveys. The nearshore survey of SAV and largemouth bass was conducted by the University of California-Davis (UC-Davis) at sites across the Delta during 2008-2010. The Aquatic Weed Control Action was completed by the Department of Water Resources as part of the Delta Smelt Resiliency Strategy and included monthly surveys of four sites during 2017-2018. The ongoing survey of Franks Tract is conducted annually by the SePRO corporation and the Division of Boating and Waterways, and available data are from 2014-2021. The ongoing annual survey conducted by the UC-Davis Center for Spatial Technologies and Remote Sensing covers many areas of the Delta and spans 2007-2008 and 2014-2021. Additional data from these ongoing surveys and data from other surveys will be added in subsequent versions of this data set.
Interagency Ecological Program: Fish catch and associated water quality for the Fall Midwater Trawl Survey, Sacramento-San Joaquin Delta, 1967-2024
The Interagency Ecological Program’s (IEP) Fall Midwater Trawl Survey (FMWT) is a long-term monitoring survey conducted by the California Department of Fish and Wildlife (CDFW) and has sampled annually since its inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT was initiated to determine the relative abundance and distribution of age-0 Striped Bass (Morone saxatilis) in the San Francisco Estuary (California, United States), but the data has also been used for other upper estuary pelagic species, including Delta Smelt (Hypomesus transpacificus), Longfin Smelt (Spirinchus thaleichthys), American Shad (Alosa sapidissima), Splittail (Pogonichthys macrolepidotus), and Threadfin Shad (Dorosoma petenense). The FMWT currently samples 130 stations each month from September to December and a subset of this data is used to calculate an annual abundance index. These 130 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, and West Sacramento on the Sacramento Deep Water Ship Channel. FMWT sampling data includes 193 unique station locations throughout the San Francisco Estuary; 63 are not currently sampled. Most stations no longer sampled occur in South and Central San Francisco Bay (1968-1979), with others located in San Pablo Bay and upstream into the Delta. There are catch records for stations that were sampled only once. Data users are encouraged to look at station frequency over time to understand when and where sampling occurred. Sampling takes approximately 14 days per month to complete. Historically, FMWT sampling occasionally began as early as July (1972) or August (1968-1973, 1993-1994, 1996-1997) and sometimes continued past December to March (1968-1973, 1978, 1991-2001) or beyond (1992-1995). The Spring Midwater Trawl (SMWT) was a modified survey created to continue sampling January-March to track movements of mature adult delta smelt from 1991-2001. SMWT was replaced in 2002 with the more e
Harmful Algal Bloom Monitoring in the Southern Sacramento-San Joaquin Delta
The Department of Water Resources (DWR) North Central Region Office (NCRO) Water Quality Evaluation Section (WQES) and the Division of Operations and Maintenance (O&M) provide technical expertise and program support for regulatory compliance, water operations, emergency response, and environmental restoration. Harmful Algal Blooms (HABs) are large overgrowths of algae in eutrophic marine or freshwater ecosystems that degrade beneficial uses of water resources, from aesthetics to habitat quality to human consumption. The Sacramento-San Joaquin Delta has observed an increasing number of HABs, especially in the South Delta. These HABs have been composed primarily of cyanobacteria, or blue-green algae (BGA). The most prevalent HAB producing cyanobacteria in recent years is the freshwater species Microcystis aeruginosa - a known producer of toxins called microcystins. Microcystins negatively affect the health of aquatic and terrestrial organisms alike, including humans and their pets. In late 2017, the Central Valley Water Resources Control Board (CVWRCB) issues a Section 401 Water Quality Certification for the DWR South Delta Temporary Barriers Projects. This certification required DWR to develop a dataset of surface Microcystis Visual Index (MVI) values during standard water quality station visits. In addition to the MVI, requirements for DWR to collect water samples for phytoplankton enumeration and cyanotoxin analysis began in 2019 and 2022, respectively. Together these data help DWR and CVWRCB to understand the distribution and composition of the algal community in the South Delta and to evaluate the species that contribute to HABs. As a separate project, DWR O&M collects cyanotoxin and taste and odor samples at Clifton Court Forebay and the Harvey O. Banks Pumping Plant to ensure that the water exported from the Delta is safe for use. This dataset provides an ongoing collection of taste and odor and cyanotoxin analysis beginning in 2009 and 2012, respectively.
Chinook Salmon genetic assignments for the Central Valley Project (CVP) and State Water Projects (SWP), Sacramento and San Joaquin Delta Waters, CA, 2024-25
Central Valley Chinook Salmon populations differ in their Endangered Species Act listing status. It is difficult to visually distinguish individuals from the different Evolutionarily Significant Units. As such, many of the salmon monitoring and evaluation efforts in the Central Valley and San Francisco Bay-Delta are hampered by uncertainty about population (stock) identification and proportional effects of management actions (Dekar et al. 2013; IEP 2019). Studies have identified that the current identification method (length-at-date models) of juvenile Chinook salmon (Fisher 1992) captured in the watershed vary in their accuracy, particularly for spring-run (NMFS 2013; Harvey et al. 2014; Merz et al. 2014). The inaccuracy of the size-based methods is likely due to differences in fish distribution during early rearing, habitat-specific growth rates, and inter-annual variability in temperatures and food availability that lead to overlap in size ranges among stocks. The primary objective of this project was the genetic classification (to genetic lineage; Evolutionary Significant Unit) of Chinook Salmon captured from State Water Project and Central Valley Project fish protection facilities and Interagency Ecological Program compliance monitoring programs. The genetic lineage was determined for sampled fish by comparing their genotypes to reference genetic baselines. Genetic methods, having less statistical uncertainty that size-based models for population identification, were intended to directly target (and reduce) one source of uncertainty in the estimation of loss (take) from water diversions (operations) and develop the information necessary for understanding stock-specific distribution, habitat utilization, abundance, and life history variation. This project supports recommendations from the Interagency Ecological Program’s Salmon and Sturgeon Assessment of Indicators by Life Stage and Interagency Ecological Program Science Agenda efforts to improve Central Valley
Interagency Ecological Program: Discrete water quality monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 1975-2023
\<markdown\> The Interagency Ecological Program’s (IEP) Environmental Monitoring Program (EMP) was initiated in compliance with the Water Right Decision D-1379 (now mandated by Water Right Decision D-1641) and has monitored discrete water quality and nutrients in the upper San Francisco Estuary since 1975. The objectives of the EMP are to obtain consistent and accurate monthly data at established monitoring stations, provide and document information necessary to achieve compliance with salinity, flow, and dissolved oxygen standards, and to report this information for the purpose of management and conservation of the upper San Francisco Estuary. While the EMP also collects biological data, this dataset only includes the discrete water quality and nutrient data collected by the EMP from 1975-2021. Links to other EMP datasets can be found [here](https://emp-des.github.io/emp-reports/data-links.html) \</markdown\>
Distribution models for riparian landbirds and waterbirds in the Sacramento-San Joaquin Delta
<p><strong>SUMMARY</strong><br> Distribution models for 9 riparian landbird species and 6 groups of waterbird species in the Sacramento-San Joaquin River Delta of California. </p> <p><strong>DESCRIPTION</strong><br> These predictive models were developed to relate the probability of species or group presence as a function of the surrounding landscape, facilitating predictions of species presence or absence over the entire landscape. Each .RData object is structured as a list containing individual model objects of class `gbm` for each species or group.</p> <p>Models were developed using Boosted Regression Trees, implemented in R using the R packages `dismo` (Hijmans et al. 2021) and `gbm` (Greenwell et al. 2020). Models were developed from pre-existing bird survey data, including 2,547 surveys for riparian landbirds conducted at 716 unique locations throughout the Central Valley of California during the breeding season (May and June), 2011–2019, and 7,820 surveys for waterbirds conducted at 504 unique locations in the Delta during the fall (July 15–November 15) and winter (November 17–March 5) seasons, 2013–14 and 2014–15. Waterbird models were developed for each of the fall and winter seasons, with 46 species grouped into 6 distinct groups defined by similar habitat requirements, foraging style, and diet. </p> <p>These models were used to predict the distribution of each species and group across a baseline Delta landscape (representing land cover in 2018), and these predictions were used to identify Priority Bird Conservation Areas in the Delta. In addition, the models were used to predict distributions for alternative scenarios of future landscape change, and to evaluate the net change from the baseline distributions in the total area of suitable habitat. These models are required for evaluating the change in Biodiversity Support benefits using the R package "DeltaMultipleBenefits", which provides the code and work flow for repeating the initial scenario analyses or analyzing new scenarios.</p> <p>For additional details about the development and applications of these data, please see: </p> <ul> <li>Dybala K, Sesser K, Reiter M, Shuford WD, Golet GH, Hickey C, Gardali T. (<em>In review</em>) Priority Bird Conservation Areas in California’s Sacramento–San Joaquin Delta.</li> <li>Dybala KE, et al. (<em>In review</em>) Multiple-benefit Conservation in Practice: A Framework for Quantifying Multi-dimensional Impacts of Landscape Change in California’s Sacramento–San Joaquin Delta.</li> <li>Dybala KE (2023) <em>DeltaMultipleBenefits: Projecting the Multiple Benefits of Land Cover Change in the Sacramento-San Joaquin River Delta</em>. R package version 1.0.0. doi:10.5281/zenodo.7718620. https://pointblue.github.io/DeltaMultipleBenefits </li> </ul> <p><strong>Literature Cited:</strong></p> <ul> <li>Greenwell B, Boehmke B, Cunningham J, Developers G (2020). <em>gbm: Generalized Boosted Regression Models</em>. R package version 2.1.8. https://CRAN.R-project.org/package=gbm</li> <li>Hijmans RJ, Phillips S, Leathwick J, Elith J (2021). <em>dismo: Species Distribution Modeling</em>. R package version 1.3-5. https://CRAN.R-project.org/package=dismo</li> </ul> <p><strong>FUNDING STATEMENT</strong><br> These data were developed as part of the project "Trade-offs and Co-benefits of Landscape Change on Bird Communities and Ecosystem Services in the Sacramento–San Joaquin River Delta", funded by Proposition 1 Delta Water Quality and Ecosystem Restoration Program, Grant Agreement Number – Q1996022, administered by the California Department of Fish and Wildlife.</p> <p><strong>POINT OF CONTACT</strong><br> Kristen Dybala, Point Blue Conservation Science, kdybala@pointblue.org</p> <p><strong>SUGGESTED CITATION</strong><br> Dybala KE, Sesser KA, Reiter ME, Shuford WD, Golet GH, Hickey CM, Gardali T. 2023. Distribution models for riparian landbirds and waterbirds in the Sacramento-San Joaquin Delta. doi: 10.5281/zenodo.7531945</p> <p><strong>DATA DISTRIBUTION</strong><br> Zenodo. (https://doi.org/10.5281/zenodo.7531945)</p> <p><strong>PROGRESS</strong><br> Complete, but note that the accompanying manuscript has not yet undergone peer-review, and thus these data may require future revision.</p> <p><strong>UPDATE FREQUENCY</strong><br> Not Planned</p> <p><strong>DATE</strong><br> These models were developed 2019-2022, based on bird survey data collected 2011-2019.</p> <p><strong>FIELD DEFINITIONS</strong><br> N/A</p> <p><strong>ABBREVIATION DEFINITIONS</strong></p> <p>BRT_models_riparianlandbirds.RData:</p> <ul> <li><strong>NUWO:</strong> Nuttall's Woodpecker (<em>Picoides nuttallii</em>)</li> <li><strong>ATFL: </strong>Ash-throated Flycatcher (<em>Myiarchus cinerascens</em>)</li> <li><strong>BHGR: </strong>Black-headed Grosbeak (<em>Pheucticus melanocephalus</em>)</li> <li><strong>LAZB: </strong>Lazuli Bunting (<em>Passerina amoena</em>)</li> <li><strong>COYE:</strong> Common Yellowthroat (<em>Geothlypis trichas</em>)</li> <li><strong>YEWA: </strong>Yellow Warbler (<em>Setophaga petechia</em>)</li> <li><strong>SPTO: </strong>Spotted Towhee (<em>Pipilo maculatus</em>)</li> <li><strong>SOSP:</strong> Song Sparrow (<em>Melospiza melodia</em>)</li> <li><strong>YBCH: </strong>Yellow-breasted Chat (<em>Icteria virens</em>)</li> </ul> <p>BRT_models_waterbirds.RData:</p> <ul> <li><strong>geese:</strong> Geese <ul> <li>Greater White-fronted Goose (<em>Anser albifrons</em>)</li> <li>Snow Goose (<em>Anser caerulescens</em>)</li> <li>Ross's Goose (<em>Anser rossii</em>)</li> <li>Cackling Goose (<em>Branta hutchinsii</em>)</li> <li>Canada Goose (<em>Branta canadensis</em>)</li> </ul> </li> <li><strong>dblr: </strong>Dabbling ducks, including: <ul> <li>Wood Duck (<em>Aix sponsa</em>)</li> <li>Gadwall (<em>Mareca strepera</em>)</li> <li>American Wigeon (<em>Mareca americana</em>)</li> <li>Mallard (<em>Anas platyrhynchos</em>)</li> <li>Blue-winged Teal (<em>Spatula discors</em>)</li> <li>Cinnamon Teal (<em>Spatula cyanoptera</em>)</li> <li>Northern Shoveler (<em>Spatula clypeata</em>)</li> <li>Northern Pintail (<em>Anas acuta</em>)</li> <li>Green-winged Teal (<em>Anas carolinensis</em>)</li> </ul> </li> <li><strong>divduck: </strong>Diving ducks (<em>Note: this model was only developed for the winter season</em>) <ul> <li>Canvasback (<em>Aythya valisineria</em>)</li> <li>Ring-necked Duck (<em>Aythya collaris</em>)</li> <li>Lesser Scaup (<em>Aythya affinis</em>)</li> <li>Bufflehead (<em>Bucephala albeola</em>)</li> <li>Common Goldeneye (<em>Bucephala clangula</em>)</li> <li>Hooded Merganser (<em>Lophodytes cucullatus</em>)</li> <li>Common Merganser (<em>Mergus merganser</em>)</li> <li>Ruddy Duck (<em>Oxyura jamaicensis</em>)</li> </ul> </li> <li><strong>crane: </strong>Cranes <ul> <li>Greater Sandhill Crane (<em>Antigone canadensis tabida</em>)</li> <li>Lesser Sandhill Crane (<em>Antigone canadensis canadensis</em>)</li> </ul> </li> <li><strong>shore: </strong>Shorebirds <ul> <li>Western Sandpiper (<em>Calidris mauri</em>)</li> <li>Least Sandpiper (<em>Calidris minutilla</em>)</li> <li>Dunlin (<em>Calidris alpina</em>)</li> <li>Black-necked Stilt (<em>Himantopus mexicanus</em>)</li> <li>American Avocet (<em>Recurvirostra americana</em>)</li> <li>Greater Yellowlegs (<em>Tringa melanoleuca</em>)</li> <li>Lesser Yellowlegs (<em>Tringa flavipes</em>)</li> <li>Long-billed Dowitcher (<em>Limnodromus scolopaceus</em>)</li> <li>Short-billed Dowitcher (<em>Limnodromus griseus</em>)</li> <li>Wilson's Snipe (<em>Gallinago delicata</em>)</li> </ul> </li> <li><strong>cicon: </strong>Herons/Egrets (Ciconiiformes) <ul> <li>Great Blue Heron (<em>Ardea herodias</em>)</li> <li>Great Egret (<em>Ardea alba</em>)</li> <li>Snowy Egret (<em>Egretta thula</em>)</li> <li>Cattle Egret (<em>Bubulcus ibis</em>)</li> <li>Green Heron (<em>Butorides virescens</em>)</li> <li>Black-crowned Night-Heron (<em>Nycticorax nycticorax</em>)</li> </ul> </li> </ul> <p><strong>ACCESS & USE CONSTRAINTS</strong><br> CC-by-4.0 (https://creativecommons.org/licenses/by/4.0/)</p> <p><strong>KEYWORDS</strong></p> <ul> <li><strong>Themes: </strong>birds, landbirds, songbirds, waterbirds, waterfowl, shorebirds, distribution, habitat</li> <li><strong>Place: </strong>Sacramento-San Joaquin River Delta, Central Valley, California</li> </ul>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.