Bed sediment samples were collected from the intertidal, and subtidal shallows of San Pablo Bay National Wildlife Refuge and Corte Madera Bay near stations where instrumented platforms that were collecting hydrographic time-series were deployed. Sediment sediments were collected with push cores, either manually or by subsampling a Gomex box corer. Cores, which ranged in length from 5 to 18 centimeters (cm), were sectioned by depth. The top two sections from each core were 0.5 cm thick, the following sections were 1 cm thick, sections below 6 cm were often sectioned either into sections that were 1 or 2 cm thick. Additional samples were taken from sediment deposited on ceramic tiles attached to the marsh surface. Samples were analyzed for sediment properties including bulk density, particle size distribution, loss on ignition, and percent carbon.

Bed sediment samples were collected from the channels of 4 sites within northern San Francisco Bay, California, USA. The channels sampled were located in Corte Madera Bay, San Pablo Bay, Grizzly Bay and Suisun Bay. Sediment samples were collected with push cores, by subsampling a Gomex box corer. Cores, which ranged in length from 2 to 6 centimeters (cm), were sectioned by depth. The top two sections from each core were 1 cm thick, the following sections were 2 cm thick. Samples were analyzed for sediment properties including bulk density, particle size distribution, and percent carbon.

Bed sediment samples were collected in San Pablo Bay and Grizzly Bays on eight days from June through November 2019, to analyze for sediment properties including bulk density, particle size distribution, and percent organic carbon. Sediment samples were collected from a small vessel near pre-established USGS instrument moorings using a Gomex box corer that was subsampled with three push cores (37 mm in diameter) per Gomex core. Six subsamples were collected from the top 5 centimeters (cm) of each push core, a few push cores included the top 8 cm. The top two subsamples were each 0.5 cm thick, and all following subsamples were each 1 cm thick. Push core samples from the first, third, and fifth centimeter depth were analyzed for grain size and percent organic carbon, while all 6 sections were analyzed for bulk density. Data are provided in a comma-delimited values spreadsheet. These data were collected as part of a collaborative project with the USGS California Water Science Center and the USGS Water Mission Area on physical and biological controls on sediment erodibility, funded by the USGS Priority Ecosystems Program for San Francisco Bay and Delta and the USGS Coastal Marine Hazards and Resources Program.

Bed sediment samples were collected in Lindsey Slough in April 2017, and Middle River and the Mokelumne River in March 2018, to analyze for sediment properties, including bulk density, particle size distribution, and percent organic carbon. Sediment samples were collected within the vegetation with push corers deployed from a small vessel, and in the unvegetated channel with a Gomex box corer, which was subsampled with three push cores per Gomex core. Data are provided in a comma-delimited values spreadsheet. These data were collected as part of a cooperative project, with the USGS California Water Science Center and the California Department of Fish and Wildlife, on the effects of invasive aquatic vegetation on sediment transport in the Sacramento-San Joaquin Delta.

Bed sediment samples were collected in San Pablo Bay and Grizzly Bays on eight days from January through September 2020, to analyze for sediment properties including bulk density, particle size distribution, and percent organic carbon. Sediment samples were collected from a small vessel near pre-established USGS instrument moorings using a Gomex box corer that was subsampled with three push cores (37 mm in diameter) per Gomex core. Six subsamples were collected from the top 5 centimeters (cm) of each push core, a few push cores included the top 8 cm. The top two subsamples were each 0.5 cm thick, and all following subsamples were each 1 cm thick. Push core samples from the first, third, and fifth centimeter depth were analyzed for grain size and percent organic carbon, while all 6 sections were analyzed for bulk density. Data are provided in a comma-delimited values spreadsheet. These data were collected as part of a collaborative project with the USGS California Water Science Center and the USGS Water Mission Area on physical and biological controls on sediment erodibility, funded by the USGS Priority Ecosystems Program for San Francisco Bay and Delta and the USGS Coastal Marine Hazards and Resources Program.

Bed sediment samples were collected in San Pablo Bay and Grizzly Bays on eight days from January through September 2020, to analyze for sediment properties including bulk density, particle size distribution, and percent organic carbon. Sediment samples were collected from a small vessel near pre-established USGS instrument moorings using a Gomex box corer that was subsampled with three push cores (37 mm in diameter) per Gomex core. Six subsamples were collected from the top 5 centimeters (cm) of each push core, a few push cores included the top 8 cm. The top two subsamples were each 0.5 cm thick, and all following subsamples were each 1 cm thick. Push core samples from the first, third, and fifth centimeter depth were analyzed for grain size and percent organic carbon, while all 6 sections were analyzed for bulk density. Data are provided in a comma-delimited values spreadsheet. These data were collected as part of a collaborative project with the USGS California Water Science Center and the USGS Water Mission Area on physical and biological controls on sediment erodibility, funded by the USGS Priority Ecosystems Program for San Francisco Bay and Delta and the USGS Coastal Marine Hazards and Resources Program.

In situ images of the sediment-water interface and sediment profiles were collected to characterize the top layer of the sediment bed (less than 15 cm sediment depth) prior to dredged material placement and post dredge material placement in south San Francisco Bay, California. Several sites within the placement area, as well as sites outside of the placement area, and near time-series stations were collected. The photos were acquired during four separate trips: August 2023 (pre-placement), October 2023 (pre-placement), January 2023 (post-placement), and February (greater than 1 year post-placement). The sediment profile imaging system consisted of a Blackfly S Board-level BFS-GE-50S5C0BD2 camera that incorporates a Sony IMX264 sensor and has an m12-mount type wide-angle 4.4 mm lens. The resulting field of view was approximately 7x15 cm at the window, with a resolution of 0.0667 mm per pixel when the vertically (portrait) oriented window of the housing was pushed into the sediment bed. The camera was secured horizontally in Sediment Profile Imaging (SPI) camera waterproof housing from OceanInstruments, which was lowered to the bay floor at the different stations and pushed from above into the sediment bed using a rigidly attached pole. The images captured using the system show a profile view which includes a surface view of the sediment bed where the window was above the water-sediment interface, and/or a high-resolution sediment profile where the window extended vertically down into the sediment bed and was flush with the sediment. The maximum depth below the water-sediment interface recorded by the sediment profile imaging camera was approximately 15 cm.

Sediment samples were collected on and adjacent to the Whale's Tail South marsh. Short push-cores of bed sediment were collected in South San Francisco Bay adjacent to Whale's Tail South marsh on five days from June through August 2021 and 3 days from November 2021 to January 2022. Additional samples were taken from sediment deposited on ceramic tiles attached to the marsh surface and from rip-up clasts deposited on the marsh edge. Samples were analyzed for sediment properties including bulk density, particle size distribution, and percent carbon.

Bed sediment samples were collected in south San Francisco Bay on two days in July 2020 to analyze for sediment grain size distributions. Sediment samples were collected from the R/V Snavely near pre-established U.S. Geological Survey instrument moorings using a Gomex or Ponar box corer that was subsampled by scraping the top 0.5 cm of the core. Data are provided in a comma-delimited values spreadsheet.

Sediment grain size was determined on one to five cm subsamples of push cores collected from the Escanaba Trough during May to June 2022.