Amy C. Foxgrover Theresa A. Fregoso Bruce E. Jaffe 20241004 GeoTIFF data release doi:10.5066/P13H35QB Pacific Coastal and Marine Science Center, Santa Cruz, CA U.S. Geological Survey https://doi.org/10.5066/P13H35QB https://www.sciencebase.gov/catalog/item/667605c1d34e3cf50fef28f6 Amy C. Foxgrover Theresa A. Fregoso Bruce E. Jaffe 2024 data release doi:10.5066/P13H35QB Pacific Coastal and Marine Science Center, Santa Cruz, CA U.S. Geological Survey Suggested Citation: Foxgrover, A.C., Fregoso, T.A., and Jaffe, B.E., 2024, Historical bathymetry and bathymetric change within San Francisco Bay, California: 1855 to 2005: U.S. Geological Survey data release, https://doi.org/10.5066/P13H35QB. https://doi.org/10.5066/P13H35QB https://www.sciencebase.gov/catalog/item/663ea8fdd34eaf9729f7b46d This data release provides a series of five bathymetric digital elevation models (DEMs) of Suisun Bay, CA generated from single-beam hydrographic surveys collected from 1866 to 1990. The DEMs were constructed based upon historical United States Coast and Geodetic Survey and National Ocean Service (NOS) surveys collected in 1866, 1886, 1923, 1941, and 1990. Depth soundings from the pre-1930s surveys were manually digitized and georeferenced while the later surveys were obtained in digital format, and all information compiled into a geographic information system (GIS). Using surface modeling software, the soundings from each survey were supplemented with hand-drawn contours and shorelines obtained from topographic sheets to generate bathymetric DEMs at a horizontal resolution of 25 m. The bathymetric DEMs are provided in GeoTIFF format, vertically referenced to the Mean Lower Low Water (MLLW) tidal epoch referenced at the time of data collection. Analysis of historical bathymetric surveys enables us to reconstruct the surface of the bay floor through time and quantify spatial and temporal changes in deposition, erosion, and bathymetry over decadal timescales. These data provide insight on changes to San Francisco Bay in response to natural processes as well as anthropogenic activities and can inform numerous studies and applications such as sediment management practices, restoration projects, regional adaptation plans, contaminant transport research, and sea-level rise studies. These data are intended for science researchers, students, policy makers, and the general public. These data can be used with geographic information systems (GIS) or other software to identify changes in the depth of the bay floor through time. These data are not intended to be used for navigational purposes. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this Federal Geographic Data Committee-compliant metadata file is intended to document the data set in nonproprietary form, as well as in Esri format, this metadata file may include some Esri-specific terminology. 1866 1990 ground condition at time data were collected Complete None planned -121.747071 -122.270970 38.1721906 38.0099650 The National Map Collection Thesaurus Digital Elevation Model (DEM) USGS Thesaurus bathymetry topography geographic information systems geospatial datasets GPS measurement digital elevation models Data Categories for Marine Planning Bathymetry and Elevation Marine Realms Information Bank (MRIB) keywords geographic information systems (GIS) single-beam echo sounder topographic mapping Global Positioning System (GPS) observations ISO 19115 Topic Category elevation inlandWaters USGS Metadata Identifier USGS:667605c1d34e3cf50fef28f6 Geographic Names Information System (GNIS) San Francisco Bay San Pablo Bay Suisun Bay None Central San Francisco Bay South San Francisco Bay No access constraints USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originator(s) of the dataset and in products derived from these data. This information is not intended for navigation purposes. U.S. Geological Survey, Pacific Coastal and Marine Science Center PCMSC Science Data Coordinator mailing and physical

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Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov https://www.sciencebase.gov/catalog/file/get/667605c1d34e3cf50fef28f6?name=SSB_bathy_map_1866.png&allowOpen=true Sample map of 1866 Suisun Bay bathymetry. PNG Microsoft Version 6.2 (Build 9200); Esri ArcGIS 10.8.1.14362(Build 9270) Service Pack N/A (Build N/A) Karen Cappiella Chris Malzone Richard E. Smith Bruce E. Jaffe 1999 Cappiella, K., Malzone, C., Smith, R, and Jaffe, B.E., 1999, Sedimentation and bathymetry change in Suisun Bay: 1867-1990: U.S. Geological Survey Open-File Report 99-563, https://pubs.usgs.gov/of/1999/0563/. https://pubs.usgs.gov/of/1999/0563 Bruce E. Jaffe Richard E. Smith Amy C. Foxgrover 2007 Jaffe, B.E., Smith, R.E., and Foxgrover, A.C., 2007, Anthropogenic influence on sedimentation and intertidal mudflat change in San Pablo Bay, California: 1856-1983: Estuarine, Coastal and Shelf Science, v. 73, no. 1–2, p. 175–187, https://doi.org/10.1016/j.ecss.2007.02.017. https://doi.org/10.1016/j.ecss.2007.02.017 International Hydrographic Organization (IHO) 2022 reference on hydrographic survey standards provided for added interest to users of these data https://iho.int/uploads/user/pubs/standards/s-44/S-44_Edition_6.1.0.pdf Environmental Systems Research Institute, Inc (Esri) 2024 https://desktop.arcgis.com/en/arcmap/latest/tools/3d-analyst-toolbox/topo-to-raster.htm No formal attribute accuracy tests were conducted. No formal logical consistency tests were conducted. Data set is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details. Data are as accurate as source data used. No further tests were conducted, and no claims are made to positional accuracy. Data are as accurate as source data used. No further tests were conducted, and no claims are made to vertical accuracy. National Oceanic and Atmospheric Administration (NOAA) 2024 xyz, tif online NOAA / NESDIS / NCEI / Maps / Seafloor Mapping https://www.ncei.noaa.gov/maps/bathymetry/ Digital Resources 1856 1989 ground condition NOAAbathy NOAA NOS single-beam surveys. 1850s to 1920s surveys available as images of NOS smooth sheets, 1930s to 1980s as digital sounding data. National Oceanic and Atmospheric Administration (NOAA) 2024 Raster Digital Dataset online NOAA / NOS https://nsde.ngs.noaa.gov/ Digital Resources 1850 1985 ground condition NOSshore NOS Topographic Sheets (T-sheets) used to delineate mean high water (MHW) shorelines used for DEM extent boundary. San Francisco Estuary Institute 1998 shapefile compact disc SFEI Digital Resources 1850 1998 ground condition SFEIshore Historical and modern baylands GIS shapefiles used to supplement shorelines extracted from T-sheets, as needed. All processes and methods used for developing the 1866, 1886, 1923, 1941, 1990 bathymetric DEMs are outlined in Cappiella and others (1999) and Jaffe and others (2007); please refer to that for more information beyond the summary in this document Jaffe and others (2007) 2006 Hydrographic sounding data downloaded for all time periods. Pre-1930s surveys were obtained as images of H-sheets that were geoferenced to NAD83 and the soundings manually digitized. Post-1930 soundings were downloaded in digital format (NOAA, 2024). The study area is covered by a compilation of hydrographic surveys that were generally conducted over the span of a few years. The year displayed with the DEMs provided is the year in which the majority of the study area was surveyed. However, the compilation of surveys covering the entire study area can span many years and end users are encouraged to view the original H-sheets and descriptive reports provided by NOAA (2024) for additional details. NOAAbathy 2006 soundings and contours Shorelines were obtained from T-sheets and assigned an approximate MHW elevation of 1.34 m based upon nearby tide stations. The 1983 shoreline was modified based upon EcoAtlas data (San Francisco Estuary Institute, 1998). NOSshore SFEIshore 2006 shorelines Bathymetric contours were digitized from H-sheets or hand drawn as needed to help define the general morphology of the bay floor and to constrain the gridding algorithm. To ensure realistic nearshore morphology, in areas where soundings were not collected within close proximity to the shoreline, an additional contour was added parallel to the shoreline, 20 m within the bay and assigned an approximate elevation of mean tide level (MTL). Supplementary contours were manually added to the 1850's tidal flats where the original sounding values have been omitted from the H-sheets. NOAAbathy NOSshore 2006 contours For each time period, soundings were combined with bathymetric contours and shoreline shapefiles and interpolated into continuous surface models with horizontal resolution of 25 m using ArcInfo's TopoGrid module (now Topo To Raster, Esri, 2024). Bathymetry in tributary channels less than 3-cells wide were excluded because they could not be accurately modeled at the given resolution. Z-values are in meters relative to the MLLW tidal epoch referenced at the time of survey collection. These grids supersede those used in Cappiella and others (1999) and have been improved through the application of consistent processing techniques throughout the entire San Francisco Bay and thousands of additional soundings added to the upated surface models that were missing from earlier analyses. NOAAbathy shorelines 2023 TopoGrid DEMs An estimate of grid interpolation bias was estimated for each time period by comparing the value of each individual sounding to the cell value of the bathymetric grid at that specific location. Each bathymetric DEM was then adjusted to correct for interpolation bias by deepening the raster surface by the mean offset value. The 1866 grid was deepened by 12.6 cm, the 1886 grid by 8.3 cm, the 1923 grid by 11.8 cm, the 1941 grid by 13.5 cm, and the 1990 grid by 6.4 cm. TopoGrid DEMs 2023 BIAS ADJ DEM Minor edits were made to the citation links in this metadata file. No data were changed. (mau@usgs.gov) 20241114 Raster pixel Universal Transverse Mercator 10 0.9996 -123.0 0.0 500000.0 0.0 row and column 25 25 Meter D North American 1983 GRS_1980 6378137.0 298.257222101 Mean Lower Low Water (MLLW) 0.01 meters Explicit elevation coordinate included with horizontal coordinates floating point Interpolation bias-corrected DEM with elevation in meters, relative to the MLLW tidal epoch referenced at the time of survey collection. Positive values represent elevations above MLLW and negative represent values below. Cells with values of -3.4028231e+38 indicate No Data. Producer defined Value Elevation relative to MLLW (m) Producer defined -43.04 1.94 meters 0.01 Interpolation bias-corrected DEM with elevation in meters, relative to the MLLW tidal epoch referenced at the time of survey collection. Since no previously established tidal epoch was available for the 1850s surveys, we have assumed that these surveys were referenced to MLLW during the months in which these surveys were collected. Positive values represent elevations above MLLW and negative represent values below. Cells with values of -3.4028231e+38 indicate No Data. The entity and attribute information were generated by the individual and/or agency identified as the originator of the data set. Please review the rest of the metadata record for additional details and information. U.S. Geological Survey - ScienceBase mailing and physical

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Denver CO 80225 US 1-888-275-8747 sciencebase@usgs.gov Files (SSB_1866bathy_MLLW_m.zip, SSB_1886bathy_MLLW_m.zip, SSB_1923bathy_MLLW_m.zip, SSB_1941bathy_MLLW_m.zip, SSB_1990bathy_MLLW_m.zip) contain bathymetric GeoTIFFs and associated TIFF world files (.tfw) for the time period indicated. Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. GeoTIFF ArcGIS 10.8.1 Zip file contains a GeoTIFF of the 1866 bathymetric DEM with associated TIFF world file (.tfw). Data can be unpacked using WinZip, or other zip decompression software. 1.0 https://www.sciencebase.gov/catalog/file/get/667605c1d34e3cf50fef28f6?name=SSB_1866bathy_MLLW_m.zip https://www.sciencebase.gov/catalog/item/667605c1d34e3cf50fef28f6 https://doi.org/10.5066/P13H35QB Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the zipped file of bathymetry data. The second link points to a landing page containing the full series of Suisun Bay bathymetric grids. The third link points to the landing page for the entire San Francisco Bay data series. GeoTIFF ArcGIS 10.8.1 Zip file contains a GeoTIFF of the 1886 bathymetric DEM with associated TIFFworld file (.tfw). Data can be unpacked using WinZip, or other zip decompression software. 0.9 https://www.sciencebase.gov/catalog/file/get/667605c1d34e3cf50fef28f6?name=SSB_1886bathy_MLLW_m.zip https://www.sciencebase.gov/catalog/item/667605c1d34e3cf50fef28f6 https://doi.org/10.5066/P13H35QB Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the zipped file of bathymetry data. The second link points to a landing page containing the full series of Suisun Bay bathymetric grids. The third link points to the landing page for the entire San Francisco Bay data series. GeoTIFF ArcGIS 10.8.1 Zip file contains a GeoTIFF of the 1923 bathymetric DEM with associated TIFF world file (.tfw). Data can be unpacked using WinZip, or other zip decompression software. 0.7 https://www.sciencebase.gov/catalog/file/get/667605c1d34e3cf50fef28f6?name=SSB_1923bathy_MLLW_m.zip https://www.sciencebase.gov/catalog/item/667605c1d34e3cf50fef28f6 https://doi.org/10.5066/P13H35QB Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the zipped file of bathymetry data. The second link points to a landing page containing the full series of Suisun Bay bathymetric grids. The third link points to the landing page for the entire San Francisco Bay data series. GeoTIFF ArcGIS 10.8.1 Zip file contains a GeoTIFF of the 1941 bathymetric DEM with associated TIFF world file (.tfw). Data can be unpacked using WinZip, or other zip decompression software. 0.6 https://www.sciencebase.gov/catalog/file/get/667605c1d34e3cf50fef28f6?name=SSB_1941bathy_MLLW_m.zip https://www.sciencebase.gov/catalog/item/667605c1d34e3cf50fef28f6 https://doi.org/10.5066/P13H35QB Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the zipped file of bathymetry data. The second link points to a landing page containing the full series of Suisun Bay bathymetric grids. The third link points to the landing page for the entire San Francisco Bay data series. GeoTIFF ArcGIS 10.8.1 Zip file contains a GeoTIFF of the 1990 bathymetric DEM with associated TIFF world file (.tfw). Data can be unpacked using WinZip, or other zip decompression software. 0.9 https://www.sciencebase.gov/catalog/file/get/667605c1d34e3cf50fef28f6?name=SSB_1990bathy_MLLW_m.zip https://www.sciencebase.gov/catalog/item/667605c1d34e3cf50fef28f6 https://doi.org/10.5066/P13H35QB Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the zipped file of bathymetry data. The second link points to a landing page containing the full series of Suisun Bay bathymetric grids. The third link points to the landing page for the entire San Francisco Bay data series. None These data can be viewed with GIS software such as ArcGIS, QGIS, or Global Mapper. 20250730 U.S. Geological Survey, Pacific Coastal and Marine Science Center PCMSC Science Data Coordinator mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998