Peter Dartnell Andrew W. Stevens Jessica R. Lacy 20250820 GeoTIFF data release DOI:10.5066/P14D723N Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey https://doi.org/10.5066/P14D723N Samantha C. McGill Jessica R. Lacy Andrew W. Stevens Rachel M. Allen Peter Dartnell Joanne C. Thede Angela C. Tan Gerald A. Hatcher 2025 data release doi:10.5066-P14D723N Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey Suggested Citation: McGill, S.C., Lacy, J.R., Stevens, A.W., Allen, R.M., Dartnell, P., Thede, J.C., Tan, A.C., and Hatcher, G.A., 2025, Hydrodynamic, bathymetric, and sediment transport data spanning dredge material placement in south San Francisco Bay, California, 2023-2025: U.S. Geological Survey data release, https://doi.org/10.5066/P14D723N. https://doi.org/10.5066/P14D723N Repeat bathymetric surveys were performed between October 2023 and January 2025 (U.S. Geological Survey field activity number 2023-655-FA) in the shallows of south San Francisco Bay, California using either a 234 kHz SwathPlus interferometric sonar or 200 kHz single beam sonar system. Gridded bathymetric surfaces derived from the processed single beam sonar data were produced with using linear interpolation. The bathymetric datasets are provided in GeoTIFF format. Repeat bathymetric data were collected between October 2023 and January 2025 to quantify the initial deposition and dispersal of fine-grained (less than 63 micron) sediment deposits formed when 73,000 cubic meters of sediment dredged from the Redwood City navigation channel was placed in the shallows of south San Francisco Bay, California. The bathymetric surveys were performed using either a 234 kHz SwathPlus interferometric side scan sonar or 200 kHz CEEHydrosystems single beam sonar system. The bathymetric surveys were conducted on October 25-26, 2023 (SwathPlus), November 16, 2023 (Single Beam), January 2, 2024 (Single Beam), January 8-9, 2024 (SwathPlus), January 23-25, 2024 (SwathPlus), March, 6-8, 2024 (SwathPlus), June 4, 2024 (Single Beam), October 15-16, 2024 (SwathPlus), January 14-15, 2025 (SwathPlus). Additional information about the field activity from which these data were derived is available online at: https://cmgds.marine.usgs.gov/fan_info.php?fan=2023-655-FA 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. 20231025 20250115 ground condition at time data were collected. Complete None planned -122.191551 -122.157713 37.609115 37.575494 USGS Metadata Identifier USGS:96fb3035-5e97-4c27-a62b-7390c8053dd6 ISO 19115 Topic Category geoscientificInformation elevation USGS Thesaurus bathymetry bathymetry measurement geospatial datasets marine geophysics sonar methods Data Categories for Marine Planning Bathymetry and Elevation Marine Realms Information Bank (MRIB) Keywords field observation none U.S. Geological Survey USGS Coastal and Marine Hazards and Resources Program CMHRP Pacific Coastal and Marine Science Center PCMSC Geographic Names Information System (GNIS) San Francisco Bay State of California none South San Francisco Bay Eden Landing Ecological Reserve 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 originators 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

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov dmp_bathy_grids.png Elevations derived from each bathymetry survey. PNG Matlab (ver. 2024a) on a Windows 11 computer. The SWATHPlus sonar system (234 kHz) depth accuracy reduces with horizontal range. The system has an estimated vertical depth uncertainty ranging from about 0.05 m to 0.34 m over a horizontal range of 0 to 90 m (www.iter-systems.com/wp-content/uploads/2020/01/IHO-standards-data-quality.pdf). The CEE Hydrosystems Ceescope single beam echosounders have a vertical accuracy of 1 cm + 1 percent of water depth (https://ceehydrosystems.com/products/single-beam-echo-sounders/ceescope/). Accuracies of final products may be lower due to total propagated uncertainties of the mapping systems, which include sonar system, position and motion compensation system, and navigation, as well as data processing that includes sounding cleaning, gridding, and datum transformations. No formal logical accuracy tests were conducted Dataset 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. The SwathPlus sonar system utilized an Applanix POS-MV was used for positioning. The Applanix POS-MV post-processed horizontal positional accuracy is about 0.1 m with roll and pitch accuracies of about 0.02 degrees (https://www.applanix.com/downloads/products/specs/posmv/POS-MV-WaveMaster-II.pdf). The Ceescope sonar systems used a Trimble BD990 dual frequency global satellite navigation system receiver for positioning during the single beam sonar surveys. Manufacturer reported accuracy in the post-processed horizontal positions from the Trimble BD990 GNSS rover trajectories is 0.8 cm + 1 ppm (https://oemgnss.trimble.com/en/products/receiver-modules/bd990), resulting in an average horizontal accuracy of 1.8 cm given an average baseline length of 10 km. Accuracies of final products may be lower due to total propagated uncertainties of the mapping systems, which include sonar system, position and motion compensation system, and navigation, as well as data processing that includes sounding cleaning, gridding, and datum transformations. The post-processed vertical positional accuracy from the Applanix POS-MV used in the SwathPlus bathymetric surveys is about 0.2 m (https://www.applanix.com/downloads/products/specs/posmv/POS-MV-WaveMaster-II.pdf). Manufacturer reported accuracy in the post-processed vertical positions from the Trimble BD990 GNSS rover trajectories is 1.5 cm + 1 ppm (https://oemgnss.trimble.com/en/products/receiver-modules/bd990), resulting in an average horizontal accuracy of 2.5 cm given an average baseline length of 10 km. Accuracies of final products may be lower due to total propagated uncertainties of the mapping systems, which include sonar system, position and motion compensation system, and navigation, as well as data processing that includes sounding cleaning, gridding, and datum transformations. All six bathymetric surveys performed with the SwathPlus sonar system were conducted using the same mapping systems and post-processed using the same methodology. The data were collected with a SWATHplus-M 234-kHz interferometric side-scan sonar system pole-mounted on the U.S. Geological Survey (USGS) R/V Parke Snavely survey vessel. During the mapping mission, an Applanix POS-MV (Position and Orientation System for Marine Vessels) was used to position the vessel, and it also accounted for vessel motion such as heave, pitch, and roll. The POS-MV also recorded position and vessel motion parameters for later post-processing. Sound-velocity profiles were collected throughout the survey days with a Castaway CTD. Post-processed POS-MV Smoothed Best Estimate of Trajectory (SBET) files were merged with the survey line files using BathySwath software and then the line files were imported into SonarWiz software. Soundings were cleaned for obvious errors and gridded into a 50-cm base surfaces. The base surfaces were exported as Erdas Imagine files in UTM Zone 10 North, WGS84 coordinates vertically referenced to the WGS84 ellipsoid. The data were transformed from WGS84 to NAD83 horizontal coordinates using ArcGIS Pro ArcTool raster projection command WGS_1984_(ITRF08)_To_NAD_1983_2011. NOAA's on-line VDATUM transformation tool states there is a +33.062 difference between WGS84 and NAVD88 elevations (vertical uncertainty of 0.06 m) at a point in the center of the survey area. A value of 33.062 was added to the original bathymetric grids to transform from WGS-84 elevations to NAVD88 elevations. The NAVD88 bathymetric grids were then exported as a GeoTIFF files in UTM zone 10, NAD83(2011) coordinates. 2025 Bathymetric surveys performed with single beam sonar systems were conducted using the same mapping systems and post-processed using the same methodology. The data were collected from personal watercraft equipped with a CEEHydrosystems Ceescope single beam sonar system with a 200 kHz and 9-degree beam angle. Initially, the survey design included a total of 40 survey lines that were oriented in the cross channel direction and spaced at 90 m intervals along channel centered on the dredged sediment placement area. The survey design was adjusted for the final single-beam survey to better characterize the sediment deposits that formed as a result of the dredged sediment placements. The updated survey design included a total of 111 cross channel transects spaced at about 23 m intervals and reduced the spatial extent of the survey area. Positions of the survey platforms were recorded at 10 Hz intervals during the mapping missions with a Trimble BD990 GNSS receiver. Sound-velocity profiles were collected throughout the survey days with a Castaway CTD. Positioning data from the GNSS receivers were post-processed using Waypoint Grafnav software to apply differential corrections from the National Geodetic Survey (NGS) Continuously Operating Reference Station Site, P222, located approximately 10 km away with horizontal and vertical coordinates relative to the North American Datum of 1983 (2011 realization). Orthometric elevations relative to the NAVD88 vertical datum were computed using NGS Geoid18 offsets. Bathymetric data were merged with post-processed positioning data and spurious soundings were removed using a custom Graphical User Interface (GUI) programmed with the computer program MATLAB. The processed data were projected using the UTM Zone 10 North meters coordinate system and continuous gridded surfaces with a horizontal resolution of 0.5 m were produced using linear interpolation. 2025 Initial inspection of the bathymetric surfaces revealed differences in elevations between the SwathPlus and single-beam surveys in regions where bathymetric change was not expected to be observed. Static vertical adjustments were therefore applied to each bathymetric surface to eliminate the mean bias based on comparisons between the initial swath survey and subsequent surveys in relatively flat areas where bathymetric change was assumed to be negligible. The mean static vertical corrections applied to the successive SwathPlus and single beam survey data were -2 cm and -13 cm, respectively. 2025 Single beam transect lines were oriented in the cross channel direction and spaced at 90 m intervals along channel centered on the dredged sediment placement area, and are comprised of 0.5 m continuous gridded surfaces. Swath survey lines went along the placement area; the distance between lines may have varied due to swath coverage dependence on water depth. Raster Grid Cell 7513 5853 1 Universal Transverse Mercator 10 0.9996 -123.00000 0.00000 500000.0 0.00 coordinate pair 0.5 0.5 Meters North American Datum of 1983, 2011 realization (NAD83(2011)) GRS80 6378137.00 298.257222101 North America Vertical Datum 1988 0.01 meters Explicit elevation coordinate included with horizontal coordinates Attribute Table Table containing attribute information associated with the data set Producer defined Elevation Elevation in meters relative to the NAVD88 vertical datum. No data value is -9999. Producer Defined -3.53648 0.109048 meters Single-beam bathymetric data from south San Francisco Bay that are gridded into 50-cm base surfaces in the UTM Zone 10 North, NAD83(2011) coordinate system. U.S. Geological Survey U.S. Geological Survey - CMGDS Mailing and Physical

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov These data are available in GeoTIFF format (.tif) format accompanied by CSDGM FGDC-compliant metadata. The survey dates and type of sonar used in the surveys are denoted in the filenames according to the following convention: yyyy_mm_dd_st_c.tif, where "yyyy" denotes the survey year, "mm" denotes the survey month, "dd" is the final day of data collection, and "st" provides the type of survey and is either "sw" for SwathPlus or "sb" for single beam. 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 ArcMap (version 10.3.1) Downloadable zip file contains the GeoTIFF (.tif) version of the bathymetry data. WinZip 51.3 https://doi.org/10.5066/P14D723N Data and metadata can be downloaded using the Network_Resource_Name link and scrolling down to the Digital Elevation Model (DEM) Data section. None. The downloadable data files have been compressed with the "zip" command and can be unzipped with Winzip (or other tool) on Windows systems. To utilize these data, the user must have software capable of uncompressing the WinZip file and importing and viewing a GeoTIFF file. 20250820 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