Samantha C. McGill 20240806 NetCDF files data release DOI:10.5066/P1XZFGCX Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey https://doi.org/10.5066/P1XZFGCX Samantha C. McGill Jessica R. Lacy Joanne C.T. Ferreira Daniel J. Nowacki Andrew W. Stevens Angela C. Tan 2024 data release DOI:10.5066/P1XZFGCX Pacific Coastal and Marine Science Center, Santa Cruz, CA U.S. Geological Survey Suggested Citation: McGill, S.C., Lacy, J.R., Ferreira, J.C.T., Nowacki, D.J., Stevens, A.W., and Tan, A.C., 2024, Hydrodynamic and sediment transport data from two marshes and adjacent shallows in Northern San Francisco Bay, California 2022-2023: U.S. Geological Survey data release, https://doi.org/10.5066/P1XZFGCX. https://doi.org/10.5066/P1XZFGCX CTD profiles were collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center to measure the physical characteristics of Corte Madera tidal creek over the course of a tidal cycle during one of the largest spring tides in both Winter and Summer. Conductivity, temperature, and pressure data were collected, as well as suspended-sediment concentration in the water column Each profile was collected from surface to bed. Profiles were collected on 4 days: August 8 and 9 of 2022 and January 19 and 20 of 2023. Data files are grouped by season (summer or winter). Users are advised to assess data quality carefully. These data were collected as part of a study with the goal to produce information useful for prioritizing marsh restoration sites, assessing restoration actions, and understanding mechanisms of sediment delivery to marshes. These data are intended for researchers, students, policy makers, and the general public. Information about the data collection field activities can be found at: https://cmgds.marine.usgs.gov/fan_info.php?fan=2022-619-FA https://cmgds.marine.usgs.gov/fan_info.php?fan=2023-603-FA Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. 20220809 20230220 ground condition at time data were collected Complete None Planned -122.5058680 -122.5050730 37.9307330 37.9302660 USGS Metadata Identifier USGS:cad4bfcb-82a1-4c39-854f-d1a2c3f47148 Global Change Master Directory (GCMD) WATER TEMPERATURE CONDUCTIVITY SALINITY DENSITY CTD Water pressure Water depth SUSPENDED SOLIDS Data Categories for Marine Planning Water Column Features USGS Thesaurus time series datasets marine water quality CTD measurement Marine Realms Information Bank (MRIB) keywords physical oceanography None U.S. Geological Survey USGS Coastal and Marine Hazards and Resources Program CMHRP Pacific Coastal and Marine Science Center PCMSC ISO 19115 Topic Category Oceans geoscientificInformation Geographic Names Information System (GNIS) San Francisco Bay Marin County State of California None Corte Madera marsh Corte Madera 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. PCMSC Science Data Coordinator U.S. Geological Survey, Pacific Coastal and Marine Science Center mailing and physical

2885 Mission Street

Santa Cruz CA 95060-5792 USA 831-427-4747 pcmsc_data@usgs.gov NBM_CTD_kayak.jpg Image of kayaker moving the kayak into position where the CTD profile will be collected. The CTD is shown on the kayak, behind the kayaker. JPEG Python 3.11.7 No formal attribute accuracy tests were conducted. Data fall within expected ranges. Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the metadata for each part of this data release carefully for additional details. Horizontal accuracy derived from GPS instrumentation is less than 1 m, however position information was recorded at the water surface prior to each profile. Displacement down current while lowering the CTD was severe during periods of high flow. Primary value of these data is to identify edge versus mid-channel locations as tidal creek width varies, as well as confirmation of the particular tidal creek observed. No formal assessment of vertical accuracy was performed. Manufacturer specification of 0.05 meter accuracy with better than 0.001 meter resolution. Conductivity, salinity, optical backscatter and pressure (CTD) data were collected in a tidal creek in Corte Madera Marsh, with an RBR maestro multi-channel logger. Profiles were collected on 4 days: August 8 and 9 of 2022 and January 19 and 20 of 2023. Data from water samples collected during this activity are available as a separate download. 20230120 The raw data files downloaded from the CTD were processed and converted to netCDF using the stglib python library, a package of code to process data consistent with procedures of the USGS Coastal/Marine Hazards and Resources Program. In stglib, attributes conforming to Climate and Forecast (CF) Conventions version 1.8 were added. All times are in Coordinated Universal Time (UTC). Corrected pressure data (P_1ac) were calculated by finding an offset with local atmospheric pressure readings when the pressure sensor was reading in air just prior to deployment. Pressure data were corrected using the offset and a time-series of local atmospheric pressure over the course of the deployment to remove the atmospheric contribution to the deployed pressure data. The resulting corrected pressure variable is the pressure due to seawater (standard_name "sea_water_pressure_due_to_seawater" in netCDF files). Data quality assurance and quality control (QAQC) was performed by inspecting all variables and replacing spurious values with NaN. Details of which portions of data were flagged and replaced are available in the metadata in each netCDF file and information about the individual QAQC trimming functions are available in the stglib documentation (https://stglib.readthedocs.io/en/latest/) in the "Instrument configuration file" section. Data not part of this study were removed during post-processing. Minor cleaning of the data was performed, as there were some instances when the CTD hit the creek bed and had mud obscuring sensors during the upcast. Users are still advised to assess data quality carefully. 20240716 Files are named with a convention that uses a multi-element alphanumeric code delimited by underscores. The first element for this dataset represents the projects name and the year it started (e.g. 'NBM22' for North Bay Marshes 2022); the second element indicates the type of data (e.g., CTD), 'a' or 'b' indicating the season, (e.g. a respresents Summer, b represents Winter); the next element 'prof' indicates the data were collected in a profiling manner; the final element ('-cal') indicates the data has been calibrated and corrected for observed atmospheric pressure variations. 20240716 GPS location was taken with a handheld GPS immediately before each CTD profile. 0.0001 0.0001 Decimal degrees D_WGS_1984 WGS_1984 6378137.0 298.257223563 NetCDF files are self-contained and attribute information may be found in the header of the file itself. The entity and attribute information was 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 - CMGDS Mailing and Physical Address

2885 Mission Street

Santa Cruz CA 95060 USA 1-831-427-4747 pcmsc_data@usgs.gov Downloadable data in netCDF format. There are two (2) different files, each containing multiple profiling days. The first three letters refer to the project name 'NBM' (North Bay Marshes); '22' refers to the year the project started (2022); An 'a' or 'b' indicates the season where 'a' is Summer and 'b' is Winter; 'prof' indicates the data are profiles; and '-cal' indicates all calibrations including atmospheric pressure correction have been applied to the data. 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. NetCDF Python 3.11.7 Files contains CTD profile data in NetCDF CF-1.8 format Netcdf CF-1.8 format 0.3028 https://doi.org/10.5066/P1XZFGCX CTD data (NBM22CTDaprof-cal.nc) may be accessed and downloaded using the Network_Resource_Name link and scrolling down to the Environmental Data section NetCDF Python 3.11.7 File contains CTD profile data in NetCDF format zip archive 0.3212 https://doi.org/10.5066/P1XZFGCX CTD data (NBM22CTDbprof-cal.nc) may be accessed and downloaded using the Network_Resource_Name link and scrolling down to the Environmental Data section None 20240806 PCMSC Science Data Coordinator U.S. Geological Survey, Pacific Coastal and Marine Science Center mailing and physical

2885 Mission Street

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