Theresa A. Fregoso Bethany Kharrazi Bruce E. Jaffe 20250723 comma-delimited text data release DOI: 10.5066/P9Y7W1ZM Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey https://doi.org/10.5066/P9Y7W1ZM Theresa A. Fregoso Amy C. Foxgrover Bethany Kharrazi Bruce E. Jaffe 2025 Data Release DOI:10.5066/P9Y7W1ZM Pacific Coastal and Marine Science Center, Santa Cruz, CA U.S. Geological Survey Suggested Citation: Fregoso, T.A., Foxgrover, A.C., Kharrazi, B., and Jaffe, B.E., 2025, Estimates of percent sand in cores collected in San Francisco Bay, California: U.S. Geological Survey data release, https://doi.org/10.5066/P9Y7W1ZM. https://doi.org/10.5066/P9Y7W1ZM Sediment analysis of cores collected in San Francisco Bay, San Pablo Bay, and the Carquinez Strait and Suisun Bay, California from 1990 to 2016 for percent sand. Handwritten core logs, x-radiographs, and the cores themselves, were examined for the presence of sand. Estimating the amount of sand made available to the estuary through erosion of the San Francisco Bay floor and sand sequestered within the system through deposition from the 1980s to 2010s for use in constructing a sand sediment budget. We utilized the bathymetric change analysis of Fregoso and others (2023) that documents sediment volume change from a 1980s bathymetric surface to a 2010s bathymetric surface, in combination with information on the sand content of the bed sediment derived from sediment cores and surface samples from six different sediment studies, to estimate the net change in sand volume in the bed of San Francisco Bay. Additional information about the field activity or activities from which these data were derived is available online at: https://cmgds.marine.usgs.gov/fan_info.php?fan=J190SF https://cmgds.marine.usgs.gov/fan_info.php?fan=J191SF https://cmgds.marine.usgs.gov/fan_info.php?fan=J200SF https://cmgds.marine.usgs.gov/fan_info.php?fan=2016-671-FA The data presented here was originally in an excel spreadsheet with one tab per core. To make this data accessible to all, the analysis for each core has been combined into one flat file with headings for each type of data presented and records for the data listed by core. It is recommended that in working with the data, the record information be separated by core and by source. 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 dataset in nonproprietary form, as well as in Esri format, this metadata file may include some Esri-specific terminology. 19900123 20161021 ground condition at time data were collected Complete None planned -122.507046 -121.863877 38.133552 37.448070 USGS Metadata Identifier USGS:99df34cd-4f03-49b1-8588-5a694fa6f15d ISO 19115 Topic Category environment inlandWaters Data Categories for Marine Planning Mining and Mineral Extraction Bathymetry and Elevation USGS Thesaurus ocean processes sedimentation ocean sciences mining and quarrying bathymetry dredging drilling and coring box coring gravity coring sediment transport estuarine processes stratigraphic thickness suspended material (water) Marine Realms Information Bank (MRIB) keywords sand deposit sediment coastal sediment budget dredge spoils disposal box coring surface sampling grab sampling sediment analysis sediment deposition sediment erosion sediment resources sediment sinks sediment sources analytical modeling conceptual modeling 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 San Pablo Bay Suisun Bay Carquinez Strait Golden Gate Pacific Ocean Alcatraz Isaland 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 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 SFBayCoreLocations.png Map depicting the location and source of cores included in this study PNG Microsoft Windows 10 Version 10.0 (Build 19045); Microsoft Excel 2302 Build 16130.20766 ; Esri ArcGIS 13.1.3.41833 Theresa A. Fregoso Bruce E. Jaffe Amy C. Foxgrover Donald Woodrow Bethany Kharrazi Kevin Orzech 2025 Fregoso, T.A., Jaffe, B.E., Foxgrover, A.C., Woodrow, D.L., Kharrazi, B., and Orzech, K., 2025, Contributions of erosion, deposition, and human activities to a change in sand storage in the bed of San Francisco Bay, California, 1980s to 2010s: U.S. Geological Survey Open-File Report 2025–1022, 30 p., https://doi.org/10.3133/ofr20251022. http://doi.org/10.3133/ofr20251022 Theresa A. Fregoso Bruce E. Jaffe Amy C. Foxgrover 2023 Fregoso, T.A., Jaffe, B.E., and Foxgrover, A.C., 2023, Bathymetric change analysis in San Francisco Bay, California, from 1971 to 2020: U.S. Geological Survey data release, https://doi.org/10.5066/P9Y5PEV0 https://doi.org/10.5066/P9Y5PEV0 While every effort was made to be precise in measurements; quality, preservation, and measurements of individual cores, determined recorded sediment intervals in core logs. Estimating the percent sand in cores from handwritten core logs is, fundamentally, subjective. Users are advised to read the companion open-file report accompanying this data release for additional information. Attributes mean the same thing throughout the data set. There are additional sediment cores that have core logs that were not included in this data release for several possible reasons, the cores was outside of this project study area, they have been released as part of another study, or the original core could not be located/determined. Data are as accurate as source data used. Users are advised to read the metadata record for the sources for horizontal accuracy details. No further accuracy tests were conducted. Data are as accurate as source data used. Users are advised to read the metadata record for the sources for horizontal accuracy details. No further accuracy tests were conducted. R.J. Anima H. E. Clifton Carol Reiss Florence L. Wong 2005 Report Table online U.S. Geological Survey https://pubs.usgs.gov/of/2005/1453/of2005-1453.pdf online report 1990 1991 ground condition A/C cores Core data for analysis of sand Donald L. Woodrow John L. Chin Florence L. Wong Theresa A. Fregoso Bruce E. Jaffe 2017 Report Table online U.S. Geological Survey https://doi.org/10.3133/ofr20171078 online report 1990 2000 ground condition A/C and Jaffe logs 1 Core logs for analysis of sand Theresa A. Fregoso Donald L. Woodrow Kevin Orzech 2024 Report Table online U.S. Geological Survey https://doi.org/10.5066/P9G7VZZQ online report 1990 2000 ground condition A/C and Jaffe logs 2 Core logs for analysis of sand Dan Allison Margaret Hampton Bruce E. Jaffe 2003 online table online U.S. Geological Survey https://pubs.usgs.gov/of/2003/0111/intro.html online report 2000 ground condition Jaffe cores Core data for analysis of sand Rene K. Takesue Mary L. McGann Thomas D. Lorenson Janet T. Watt 2021 csv online U.S. Geological Survey https://doi.org/10.5066/P9BDEB3K online resources 2016 ground condition Watt cores Core data for analysis of sand Donald Yee Bryan Bemis Douglas Hammond Wes Heim Bruce E. Jaffe Anthony Rattonetti Saskia. van Bergen 2011 online table online San Francisco Estuary Institute https://www.sfei.org/sites/default/files/biblio_files/652-Coring-2006-Yee-report-Final-web.pdf online resources 2006 ground condition Yee cores Core data for analysis of sand Cores taken in San Francisco Bay were divided into the following bays: South Bay, Central Bay, San Pablo Bay and Suisun Bay. Each core was logged in one or several of the following ways prior to this effort: paper logs based on observations of the working/archived core, graphic illustrated logs included in various reports, and grain size tables included in reports and open file reports. The intervals chosen and qualitative findings of sand reported are drawn directly from the paper logs, as they have the most detail in describing units and illustrating sand presence. The paper logs were obtained electronically (some were included in open file reports) or physically in labeled binders at USGS Menlo Park. The other logging methods were used as secondary confirmations of the paper log content. For just a few cores, the secondary logs did not line up with the paper log. These cores were visited in person to confirm the mismatch. Where sand was described in the written portion of the paper logs and/or drawn in the visual depiction of the core, percent sand was estimated. The illustration of the core helped contextualize the distribution and thickness of sand in the units. Several paper logs included a written percent sand estimate, which was then reported in the spreadsheet for this effort. Where there was not a percent sand estimate, various methods were used to estimate sand presence in the units. If a unit contained sand laminae, then they were counted and estimated for thickness from the visual depiction of the core and associated descriptions to determine the amount of sand in the unit. If a unit contained sand interbeds or lenticular bedding, a similar process was used depending on the thickness of each bed. Where there were sand-filled burrows, an estimation was made based on the frequency and distribution of the burrows and their apparent thickness drawn on the paper log. If a unit was described at “Muddy Sand”, “Sandy Mud”, or any other description in which sand was either a matrix or a secondary grain size in any unit and not clearly distinguished visually on the paper log (i.e., sand was noted in the description but not visually marked in any identifiable way on the drawn core), a best estimation was made based on the description. Percent sand for intervals was calculated by dividing the total amount of sand in centimeters from the length of the unit in centimeters and multiplying by 100. Percent sand was estimated for the entire core when at least one unit contained sand. This was calculated by adding up the amount of sand in every unit and then dividing the sum by the length of the core. If a core had any gaps, these were subtracted from the overall length of the core. A/C cores A/C and Jaffe logs 1 A/C and Jaffe logs 2 Jaffe cores Watt cores Yee cores 20210626 Point Point 186 0.00001 0.00001 Decimal degrees World Geodetic System 1984 (WGS84) WGS84 6378137.0 298.257223563 Attribute Table Table containing attribute information associated with the dataset Producer defined Core The core ID producer defined For A/C cores, the core IDs begin with of the last two numbers of the year collected, followed by a dash and sequential numbers assigned on day of collection. For Jaffe cores, cores begin with BC for box cores, or GC or GCC for gravity cores, followed by a dash and sequential numbers assigned on day of collection. Watt cores begin with SPB followed by sequential numbers assigned on day of collection. Yee cores begin with initials representing subembayment (SB – south bay, LSB – lower south bay, SU – Suisun, CB – Central Bay, SPB – San Pablo Bay), followed either by sequential numbers assigned on day of collection or more descriptive place name. Source The sources of the information for the rest of the attribute values producer defined paper log data taken from a handwritten core log Producer defined note Specific detail about record Producer defined core length, recorded length of core Producer defined graphic log digital representation of a core log Producer defined Date_logged Date core was logged, day/month/year, or year only. -9999 used when date not known. producer defined 2/10/2003 11/4/2020 Date in month/day/year format or year Interval_top_cm the location of the top of current interval in the specified core. -9999 represents data records where core interval does not apply. producer defined 1 368 cm 0.1 Interval_bottom_cm the location of the bottom of current interval in the specified core. -9999 represents data records where core interval does not apply. producer defined 1 372 cm 0.1 Interval_length Length of interval in the specified core. -9999 represents data records where core length does not apply. producer defined 1 372 cm 0.1 Sand_pct the measured percent of sand by volume as a decimal for the interval record, -9999 indicates that this value does not apply to record column. producer defined 0.00 1 decimal percent 0.0001 Min_pct the minimum percent by volume as a decimal of sand for the interval record, -9999 indicates that this value does not apply to record column. producer defined 0.0000 1.0000 decimal percent 0.0001 Max_pct the maximum percent by volume as a decimal of sand for the interval record, -9999 indicates that this value does not apply to record column. producer defined 0.0000 1.0000 decimal percent 0.0001 Notes Notes on sediment type for the specific interval. producer defined Notes on sediment type for the specific interval, na represents no applicable data. Comments Any relevant notes to interval producer defined Any relevant notes, na represents no applicable data cm_sand The thickness of the sand layer in the interval. This value divided by the length of the interval in which it appears, is the calculated percent sand for the interval. -9999 was used for records where data were not relevant. producer defined 0 64 cm 0.1 XWGS84 longitude, No data values -9999 producer defined -122.47317 -122.030 90 degree YWGS84 latitude, No data values -9999 producer defined 37.45950 38.10355 degree XUTM83 X UTM NAD83 zone 10 north. No data values -9999 producer defined 546303.6232 585012.344 meters YUTM83 y UTM NAD83 zone 10 north. No data values -9999 producer defined 4146268.693 4217483.725 meters Bay Subembayment where core is located producer defined Suisun Subembayment Producer defined San Pablo Subembayment Producer defined Central Subembayment Producer defined South Subembayment Producer defined Lower South Subembayment Producer defined na no applicable data Producer defined Year Year of core collection producer defined 1990 2016 year Equipment Coring method producer defined Box Coring method Producer defined Gravity Coring method Producer defined Vibracore Coring method Producer defined na no applicable data Producer defined Survey survey reference producer defined Anima/Clifton 1990 and 1991 Anima and Clifton survey cruises Producer defined Jaffe 2000 Jaffe survey cruise Producer defined Watt 2016 Watt survey cruise Producer defined Yee 2006 Yee survey cruise Producer defined na no applicable data Producer defined The first line of the csv file is a header line. U.S. Geological Survey U.S. Geological Survey - CMGDS mailing and physical

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Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov These data are available in csv format accompanied by CSDGM FGDC-compliant metadata. 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. comma-delimited text Microsoft Excel 2302 Build 16130.20766 cvs table No compression applied 0.299 https://doi.org/10.5066/P9Y7W1ZM Data and metadata can be downloaded using the Network_Resource_Name link and scrolling down to the Data section. None. These data can be viewed with any spreadsheet or word processing software capable of opening CSV files. 20250723 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 Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998