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The goal of this study was to develop a suite of inter-related water quality monitoring approaches capable of modeling and estimating the spatial and temporal gradients of particulate and dissolved total mercury (THg) concentration, and particulate and dissolved methyl mercury (MeHg), concentration, in surface waters across the Sacramento / San Joaquin River Delta (SSJRD). This suite of monitoring approaches included: a) data collection at fixed continuous monitoring stations (CMS) outfitted with in-situ sensors, b) spatial mapping using boat-mounted flow-through sensors, and c) satellite-based remote sensing. The focus of this specific Child Page is to present all field and laboratory-based data associated with...
Categories: Data;
Tags: Lower Sacramento,
San Francisco Bay,
San Joaquin Delta,
chemical analysis,
datasets,
This project designed a monitoring program and protocol to detect the effects of climate change on tidal marsh bird population abundance and distribution. It is a companion to “Tidal Marsh Bird Population and Habitat Assessment for San Francisco Bay under Future Climate Change Conditions” and will build on its products, enabling evaluation of the long-term viability of four tidal-marsh bird species threatened by impacts of climate change: Clapper Rail, Black Rail, Common Yellowthroat, and Song Sparrow (three endemic subspecies: San Pablo, Suisun, and Alameda). Information is available through the California Avian Data Center. See also: http://data.prbo.org/apps/sfbslr/index.php?page=lcc-page
Categories: Data,
Project;
Tags: 2010,
CA,
California Landscape Conservation Cooperative,
Conservation NGOs,
Datasets/Database,
The Sacramento / San Joaquin River Delta (SSJRD) is contaminated with legacy mercury (Hg) from historical mining and mineral processing activities throughout the watershed, as well as from contemporary atmospheric and industrial inputs. The current project was designed for the purpose of developing high-resolution spatial and temporal models for estimating concentrations of mercury species in surface waters of the SSJRD. The field component of the project brings together three high-resolution platforms for collecting water-quality data (fixed continuous monitoring stations (CMS) outfitted with in-situ sensors, spatial mapping using boat-mounted flow-through sensors, and satellite-based remote sensing) coupled with...
Categories: Data;
Tags: California,
Environmental Health,
Geochemistry,
Lower Sacramento,
Remote Sensing,
Sediment particles can strongly bind metals, effectively repartitioning them from solution to a solid phase. As a result, sediments may accumulate and retain metals released to an aquatic environment. Sediment cores provide a historical record of metal inputs that can reveal anthropogenic influences (Förstner and Wittmann, 1979). Specifically, studies of sediment cores in San Francisco Bay chronicled metal inputs and suggested that legacy contamination can remain a chronic source of metals to the system owing to sediment mixing and redistribution (Hornberger and others, 1999; Van Geen and Luoma, 1999). Metals in sediments also indicate exposure levels to benthic animals through contact with, and ingestion of, bottom...
Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail ( Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11...
Categories: Data;
Types: Citation,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Clapper Rail,
Fragmentation,
Microsatellites,
Population declines,
Ridgway’s rail,
Estuaries provide critical habitat for a vast array of fish and wildlife but are also a nexus for core economic activities that mobilize and concentrate contaminants that can threaten aquatic species. Selenium (Se), an essential element and potent reproductive toxin, is enriched in parts of the San Francisco Estuary (SFE) to levels known to cause toxicity, yet the risk of Se to species that inhabit the SFE is not well understood. We quantified Se concentrations in muscle, liver, and ovary of the demersal cyprinid Sacramento Splittail from six regions in the SFE at three time points (fall 2010-11, spring 2017) to evaluate Se exposure risk. Here we report fish morphological attributes, total selenium concentrations...
The dataset includes three separate excel spreadsheets which provides waterbird (and predator) observations within individual survey units during the May 2019 breeding waterbird survey of south San Francisco Bay (2019WaterbirdSurveyFullData.xlsx), the total number of American avocets, black-necked stilts, and Forster's terns within each pond unit surveyed during the May 2019 survey (2019WaterbirdSurveyPondModel.xlsx), and the annual total number of nests for American avocets, black-necked stilts, and Forster's terns in south San Francisco between 2005 and 2019 (SouthBayWaterbirdNests2005-2019.xlsx). These data support the following publication: Hartman, C.A., Ackerman, J.T., Schacter, C.R., Herzog, M.P., Tarjan,...
Categories: Data;
Tags: San Francisco Bay,
USGS Science Data Catalog (SDC),
Wildlife Biology,
biota,
birds,
This portion of the data release presents orthomosaic images of the Whale's Tail Marsh region of South San Francisco Bay, CA. The orthomosaics have resolutions of 2.5 centimeters per pixel and were derived from structure-from-motion (SfM) processing of repeat aerial imagery collected from fixed-wing aircraft. The raw imagery used to create these elevation models was acquired from an approximate altitude of 427 meters (1,400 feet) above ground level (AGL), using a Hasselblad A6D-100c camera fitted with an HC 80 lens, resulting in a nominal ground-sample-distance (GSD) of 2.5 centimeters per pixel. The acquisition flight lines were designed to provide approximately 50 percent overlap between adjacent flight lines...
Categories: Data;
Tags: Alameda County,
Alameda Creek,
Bathymetry and Elevation,
CHMRP,
Coastal and Marine Hazards and Resources Program,
The urbanized area of downtown Menlo Park is subject to persistent flooding and sediment deposition by San Francisquito Creek in South San Francisco Bay. To mitigate these events, a suite of cores was collected in 2002 at the mouth of the creek to determine sediment depositional rates on the delta. One of those cores (721-1) was selected for microbiological (pollen, diatoms, and foraminifera) and geochemical analyses to reconstruct a depositional record over the past two millennia. This data release provides radiocarbon dates, census counts of benthic foraminifera, diatoms, and palynomorphs, and the measurement of anthropogenic metals and other elements in sediments from this core.
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: CMHRP,
Coastal and Marine Hazards and Resources Program,
Habitat,
Hooks Point,
Invertebrates,
These data present suspended particle size distributions collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center within two embayments of San Francisco Bay. Data were collected at one site in San Pablo Bay and one site in Grizzly Bay from January through February 2020 by deploying a Sequoia Scientific Laser In-situ Scattering and Transmissometry instrument (LISST 200x) from a small vessel near pre-established USGS instrument moorings. At both sites, data were collected on four dates at three depths, generally near the water surface, at mid depth, and near the sediment bed, for 1-3 minutes at each depth. LISST volume concentrations are most accurate when the optical percent transmission...
Water samples were collected in San Pablo Bay and Grizzly Bay on five days from January through June 2020. The water samples were collected from a small vessel near pre-established USGS instrument moorings using a peristaltic pump or a Niskin bottle. Data are provided in a comma-delimited values spreadsheet.
Categories: Data;
Tags: CMHRP,
Coastal and Marine Hazards and Resources Program,
Grizzly Bay,
PCMSC,
Pacific Coastal and Marine Science Center,
A one- and two-dimensional hydrodynamic model of the San Francisco Bay and Delta was constructed using the Delft3D Flexible Mesh Suite (Delft3D FM; Kernkamp and others, 2011; https://www.deltares.nl/en/software/delft3d-flexible-mesh-suite/) to simulate still water levels. Required model input files are provided to run the model for the time period from October 1, 2018, to April 30, 2019. This data release describes the construction and validation of the model application and provides input files suitable to run the model on Delft3D FM Suite 2020.04. Model Description The San Francisco Bay and Delta Still Water Level Model (SFBD-SWL) utilizes the open-source Delft3D Flexible Mesh Suite (Delft3D FM; Kernkamp and...
This 50-m-resolution surface presents bathymetric change of South San Francisco Bay, California (hereafter referred to as South Bay). This surface compares a 1-m-resolution digital elevation model (DEM) of the southern portion of San Francisco Bay (Fregoso and others, 2021), comprised of bathymetry data in the South Bay region from the time period referred to as the 2010s because the majority of the surveys were in that decade, to a 50-m-resolution DEM of South Bay comprised of historic surveys from 1979 to 1985 (referred to as the 1980s because the majority of the surveys were in that decade). The creation of this change surface involved the resampling of the 1-m-resolution 2010s DEM to match the 50-m-resolution...
Categories: Data;
Tags: Bathymetry and Elevation,
GPS measurement,
Global Positioning System (GPS) observations,
San Francisco Bay,
South Bay,
Hydrodynamic and sediment transport time-series data, including water depth, velocity, turbidity, conductivity, and temperature, were collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center within two embayments of San Francisco Bay. Data were collected in San Pablo Bay and Grizzly Bay from June to August 2019 at seven unique stations. Data files are grouped by area (shallows of San Pablo Bay, channel of San Pablo Bay, and shallows of Grizzly Bay). Each shallow site contained a variety of sensors located on two tripods and one surface mooring, while the channel site consisted of one tripod. Users are advised to assess data quality carefully, and to check metadata for instrument information,...
A 1-m resolution, continuous surface, bathymetric digital elevation model (DEM) of the southern portion of San Francisco Bay, was constructed from bathymetric surveys collected from 2005 to 2020. In 2014 and 2015 the California Ocean Protection Council (OPC) contracted the collection of bathymetric surveys of large portions of San Francisco Bay. A total of 93 surveys were collected using a combination of multibeam and interferometric side-scan sonar systems. Of those 93 surveys, 75 consist of swaths of data ranging from 18- to just over 100-meters wide. These swaths were separated by data gaps ranging from 10- to just over 300-meters wide. The no-data areas required interpolation to create a continuous surface....
This project evaluates the effects of global climate change and sea level rise on estuarine intertidal habitat in the San Francisco Bay and the Pacific Flyway migratory waterbirds that rely on this habitat. Phase 2 of this project is a continuation of work to evaluate the effects of global climate change and sea level rise (SLR) on intertidal shoals in the San Francisco Bay Estuary and the migratory waterbirds that rely on this critically important resource in the Pacific Flyway. The primary objectives are to: 1) use downscaled global climate change models to translate SLR and climate scenarios into habitat quantity predictions through Delft3D and Dflow-FM (unstructured grid) geomorphic modeling; 2) model the response...
Categories: Data,
Project;
Tags: 2010,
2012,
Applications and Tools,
CA,
California Landscape Conservation Cooperative,
The dataset documents the spatial and temporal variability of nutrients and related water quality parameters at high spatial resolution in the San Francisco Bay of California, USA in 2021 and 2022. The dataset includes nitrate, temperature, conductivity, dissolved oxygen, and chlorophyll as well as information about phytoplankton community composition. Data-collection cruises were conducted under different environmental/flow conditions. Version history: On 3/15/24, the provisional data files hosted on this webpage were removed, and replaced with updated finalized files.
Categories: Data;
Tags: California,
San Francisco Bay,
San Pablo Bay,
Suisun Bay,
USGS Science Data Catalog (SDC),
Remote sensing based maps of tidal marshes, both of their extents and carbon stocks, have the potential to play a key role in conducting greenhouse gas inventories and implementing climate mitigation policies. Our objective was to generate a single remote sensing model of tidal marsh aboveground biomass and carbon that represents nationally diverse tidal marshes within the conterminous United States (CONUS). To meet this objective we developed the first national-scale dataset of aboveground tidal marsh biomass, species composition, and aboveground plant carbon content (%C) from six CONUS regions: Cape Cod, MA, Chesapeake Bay, MD, Everglades, FL, Mississippi Delta, LA, San Francisco Bay, CA, and Puget Sound, WA....
Categories: Data;
Tags: C-band synthetic aperture radar,
Cape Cod,
Chesapeake Bay,
National greenhouse gas inventory,
Puget Sound,
Habitat projections from the WARMER-2 model for four tidal wetland sites in San Francisco Bay estuary under the constant sediment scenario, plus 0.2 ppt per decade salinity scenario, and the community transition organic productivity function under a 99 cm by 2100 sea-level rise scenario. Results are the average from one hundred Monte Carlo simulations.
A 1-m resolution, continuous surface, bathymetric digital elevation model (DEM) of the northern portion of San Francisco Bay, which includes San Pablo Bay, Carquinez Strait, and portions of Suisun Bay, was constructed from bathymetric surveys collected from 1999 to 2016. In 2014 and 2015 the California Ocean Protection Council (OPC) contracted the collection of bathymetric surveys of large portions of San Francisco Bay. A total of 93 surveys were collected using a combination of multibeam and interferometric side-scan sonar systems. Of those 93 surveys, 75 consist of swaths of data ranging from 18- to just over 100-meters wide. These swaths were separated by data gaps ranging from 10- to just over 300-meters wide....
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