Metadata: Identification_Information: Citation: Citation_Information: Originator: Samantha C. McGill Originator: Joanne C.T. Ferreira Originator: Daniel J. Nowacki Originator: Jessica R. Lacy Publication_Date: 20240806 Title: Hydrodynamic time-series data from two marshes and adjacent shallows in Northern San Francisco Bay, California, 2022-2023 Geospatial_Data_Presentation_Form: NetCDF files Series_Information: Series_Name: data release Issue_Identification: DOI:10.5066/P1XZFGCX Publication_Information: Publication_Place: Pacific Coastal and Marine Science Center Santa Cruz, California Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/P1XZFGCX Larger_Work_Citation: Citation_Information: Originator: Samantha C. McGill Originator: Jessica R. Lacy Originator: Joanne C.T. Ferreira Originator: Daniel J. Nowacki Originator: Andrew W. Stevens Originator: Angela C. Tan Publication_Date: 2024 Title: Hydrodynamic and sediment transport data from two marshes and adjacent shallows in Northern San Francisco Bay, California 2022-2023 Series_Information: Series_Name: data release Issue_Identification: DOI:10.5066/P1XZFGCX Publication_Information: Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, California Publisher: U.S. Geological Survey Other_Citation_Details: 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. Online_Linkage: https://doi.org/10.5066/P1XZFGCX Description: Abstract: Hydrodynamic and sediment transport time-series data, including water depth, velocity, turbidity, conductivity, and temperature, were collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center at shallow subtidal and intertidal sites in Corte Madera Bay and San Pablo Bay National Wildlife Refuge (SPNWF) in San Francisco Bay, CA, as well as on the marsh plain of SPNWF marsh and in a tidal creek and on the marsh plain of Corte Madera Marsh, in 2022 and 2023. Data files are grouped by station, San Pablo subtidal, San Pablo intertidal, San Pablo marsh, Corte Madera subtidal, Corte Madera intertidal, Corte Madera marsh, or Corte Madera tidal creek, then by instrument type. At most stations there were periods of low water when sensors were no longer submerged, resulting in spurious data. In addition, most instruments experienced some degree of biofouling, particularly at the subtidal and intertidal stations. The subtidal stations also occasionally show signs of platform rocking or movement due to strong water flow, and/or from accidental fisher/boater interference. Users are advised to assess data quality carefully, and to check the metadata for instrument information, as platform deployment times and data-processing methods varied. Purpose: The data were collected to determine the relationship between SSC in the shallows and sediment deposition at two different marshes, during a range of tidal, wave, and hydrologic conditions. The goals of the project are 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. Supplemental_Information: Additional information about the field activities from which these data were derived is available online 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. Image maps showing locations of sampling sites are located with the Supplemental files accompanying this dataset. Tables of filenames and contents as well as calibration data for optical instruments are also included. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20220414 Ending_Date: 20230828 Currentness_Reference: Ground condition at time data were collected. Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -122.5055250 East_Bounding_Coordinate: -122.4749500 North_Bounding_Coordinate: 38.1144300 South_Bounding_Coordinate: 37.9301300 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:f5ac7033-3b7e-45b9-8f62-1a966e19577b Theme: Theme_Keyword_Thesaurus: Global Change Master Directory (GCMD) Theme_Keyword: Water depth Theme_Keyword: Water pressure Theme_Keyword: Sediment transport Theme_Keyword: Tidal currents Theme_Keyword: Water temperature Theme_Keyword: Conductivity Theme_Keyword: Salinity Theme_Keyword: Turbidity Theme_Keyword: Tidal height Theme_Keyword: Pressure sensors Theme_Keyword: Wave height gauges Theme_Keyword: CTD Theme_Keyword: Aquatic ecosystems Theme: Theme_Keyword_Thesaurus: Data Categories for Marine Planning Theme_Keyword: Water-Quality Parameters Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: oceans Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: time series datasets Theme_Keyword: CTD measurement Theme_Keyword: marine water quality Theme_Keyword: suspended material (water) Theme: Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords Theme_Keyword: seabed Theme_Keyword: field observation Theme_Keyword: wave observations Theme_Keyword: water level measurements Theme_Keyword: physical oceanography Theme: Theme_Keyword_Thesaurus: none Theme_Keyword: U.S. Geological Survey Theme_Keyword: USGS Theme_Keyword: Coastal and Marine Hazards and Resources Program Theme_Keyword: CMHRP Theme_Keyword: Pacific Coastal and Marine Science Center Theme_Keyword: PCMSC Theme_Keyword: Shallow-water habitat Theme_Keyword: Tidal shallows Place: Place_Keyword_Thesaurus: Geographic Names Information System (GNIS) Place_Keyword: San Francisco Bay Place_Keyword: Marin County Place_Keyword: Sonoma County Place_Keyword: State of California Place_Keyword: San Pablo Bay Place: Place_Keyword_Thesaurus: none Place_Keyword: Corte Madera marsh Place_Keyword: San Pablo Bay National Wildlife Refuge Place_Keyword: Corte Madera Bay Access_Constraints: No access constraints Use_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. Point_of_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Person: PCMSC Science Data Coordinator Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060-5792 Country: US Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Browse_Graphic: Browse_Graphic_File_Name: NBM_timeseries_stations_map_v1.png Browse_Graphic_File_Description: Map showing the locations of each station where time-series data were collected. Browse_Graphic_File_Type: PNG Data_Quality_Information: Attribute_Accuracy: Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted. Data were collected in a complex and changing physical environment. Sites are intermittently inundated and affected by tidal and atmospheric variation. Instruments at the same site are submerged or partially submerged at varying times. Ambient air temperature, as well as water temperature, may affect measurements. Biological fouling may have impacted data quality. Data are raw unless noted in the netCDF file metadata, as the removal of bad data is highly interpretative and may result in a loss of information, preventing further analysis and understanding. Individual instrument accuracy can be found on each manufacturer’s website. Logical_Consistency_Report: No formal logical accuracy tests were conducted. Data fall within expected ranges, however due to the intermittent and gradual inundation of tidal and marsh sites, some measurements will be in air while others are in water (including at the same site). Data spikes that reflect the changing conditions have been retained as the assessment of data quality and accuracy may be useful in interpretation and analysis. Completeness_Report: Dataset is considered complete for the information presented, as described in the abstract. Data outside of the deployment and recovery times have been removed. Users are advised to read the metadata in each netCDF file carefully for additional details affecting individual instruments and sensors. Positional_Accuracy: Horizontal_Positional_Accuracy: Horizontal_Positional_Accuracy_Report: Horizontal accuracy derived from GPS instrumentation is less than 1 m. Vertical_Positional_Accuracy: Vertical_Positional_Accuracy_Report: There are two sources of uncertainty associated with vertical positioning of the instruments: 1) the measuring tools used during instrument mounting, 2) the amount of settling that occurs during deployment. No corrections were made to the data to account for these errors. Users may refer to the pre-deployment sensor heights provided in the datafiles in addition to the nominal heights of the sensors which are also found in the data files to verify changes in sensor elevation. The heights provided do not account for any sinking that may have occurred during the deployment. Lineage: Process_Step: Process_Description: Two quadpod platforms were deployed in Northern San Francisco Bay, one in the subtidal shallows of Corte Madera Bay, and a second in the subtidal shallows of San Pablo Bay National Wildlife Refuge. Platforms were turned roughly every 60 days, equating to eight total deployments, named A through H. Each of the two subtidal stations (named PS and CS) included a Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter, and an RBR CTD. Both turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling. Process_Date: 20230717 Process_Step: Process_Description: Two weightstand (flat weight with center pole) platforms were deployed in Northern San Francisco Bay, one in the intertidal shallows of Corte Madera Bay, and a second in the intertidal shallows of San Pablo Bay National Wildlife Refuge. Platforms were turned roughly every 60 days, equating to nine total deployments, named A through I. Each of the two intertidal stations (named PI and CI) included an RBR bursting pressure sensor and a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger. Both turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling. Process_Date: 20230828 Process_Step: Process_Description: Two marsh-top platforms, CM and PM, were deployed at Corte Madera Marsh and San Pablo National Wildlife Refuge Marsh, both were positioned directly in line with the intertidal and subtidal sites, at approximately 25 m back from the bay edge. The bay edge was defined as the end of marsh vegetation and start of mudflat. Both platforms included a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger, as well as an RBR logger measuring pressure attached to rebar above the marsh surface. Both Seapoint turbidity meters were equipped with Zebra-Tech hydro-wipers to prevent biofouling. Platforms were turned roughly every 60 to 90 days, equating to eight total deployments for CM, named A through H, and five total deployments for PM, named A, C, D, F, and H. Process_Date: 20230718 Process_Step: Process_Description: One platform, CC, consisting of a Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter and a RBR pressure logger were attached to a grate that was deployed directly onto the bottom surface of the channel of a tidal creek located in Corte Madera Marsh. The turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling and had a wire cage placed around it, outside of the sensors sample volume, to keep floating debris from catching or damaging the sensor. The platform was turned roughly every 60 days, equating to eight total deployments, named A through H. Process_Date: 20230718 Process_Step: Process_Description: All recovered data from the retrieved instruments were post-processed using manufacturers software packages and USGS MATLAB codes or USGS Python codes. Process_Date: 20240506 Process_Step: Process_Description: Data were accumulated into NetCDF files. During post-processing, data collected before deployment and after recovery were removed. Bad data points identified by 1) the deployment and recovery times, 2) data flagged as erroneous by the manufacturer, 3) amplitude or correlation values outside of predetermined quality thresholds for the velocimeter were removed, as were data where pitch and roll exceeded 25 degrees. The files include data of intermittent poor quality due to various reasons which may include but are not limited to biofouling, movement of platform, and exposure during low tides. Despite removal of bad data, some are still present in the files and therefore judgment should be applied when using them, as with all other data files. Use of all data requires careful assessment of data quality. Process_Date: 20240506 Process_Step: Process_Description: For each turbidity sensor, a linear least-squares regression with intercept of zero was made between the turbidity values (in NTU or volts) and sample suspended sediment concentration (SSC) values (in milligrams per liter) from in situ measurements coincident to water sample collection. These constants are available as a support file in this data release NBM_Turbidity_to_SSC_calibration_constants.csv. Users should also note the gain setting used when applying a calibration coefficient to the turbidity data, all turbidity to SSC calibration constants were based on 5x gain setting. Process_Date: 20240506 Process_Step: Process_Description: All pressure data were given a new variable P_1ac, that contains atmospherically corrected pressure data. For this correction, the residual difference between the in-air reading of the pressure sensor and the NOAA station was removed, and is noted in the netCDF file as atmospheric_pressure_correction_offset_applied. Process_Date: 20240506 Process_Step: Process_Description: Wave statistics were calculated from the bursts of velocity and pressure measured by the ADV and from the bursts of pressure measured by the RBR bursting pressure logger. Calculations were completed using routines available on https://code.usgs.gov/cmgp/stglib. Additional information on frequency cutoffs used for the calculations can be found in the metadata of the nc data file. Process_Date: 20240506 Process_Step: Process_Description: Files were named with a convention that uses a 12- to 15-digit alpha-numeric code. The first three characters for this dataset are all 'NBM' indicating the experiment name; the fourth and fifth positions represent the calendar year in which the project commenced (22, 2022); the sixth character is a letter representing the embayment (S, San Pablo; C, Corte Madera); the seventh character is a letter representing the station's location (M, marsh; C, tidal creek; I, intertidal; S, subtidal); the eight character is a letter corresponding to the deployment (A through I, where A is the first deployment); the ninth and tenth characters represent the instrument position on the platform, where 01 is the top-most. The eleventh, twelfth, and sometimes thirteenth characters are abbreviations for the instrument type (vec, Norteks Acoustic Doppler Velocimeter; aq, Nortek aquadopp acoustic doppler current profile; pt, RBRs bursting pressure sensor with temperature; pr, RBRs pressure sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger). There are an additional 1 to 4 characters with a hyphen used to convey information about the data contained in the file. Filenames containing (-a) were used for instruments with singular/averaged observations, the (-a) also appears in the vector filenames to indicate that the file includes the burst data, while filenames with (-s) indicate the statistics/burst averaged observations of the data for bursting instruments. Similarly, (s-a) indicates the file contains wave statistics. For the bursting pressure sensors only (b-cal) indicates the file contains the burst data, and that those pressure data were corrected for atmospheric pressure. Information on the files available for each station and the data each file contains is listed in the NBM_time_series_file_table.csv. Process_Date: 20240506 Process_Step: Process_Description: The netCDF files were compressed and combined in zipped files. Files were grouped by station (San Pablo Subtidal, Intertidal, Marsh, Corte Madera Subtidal, Intertidal, Marsh or Tidalcreek) and then by instrument type. Instrument type suffixes follow the nomenclature defined above for filenames including a two- or three-character code for the instrument type (vec, Norteks Acoustic Doppler Velocimeter; aqd, Nortek aquadopp acoustic doppler current profile; pt, RBRs pressure sensor with temperature; pr, RBRs pressure sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger). Process_Date: 20240531 Spatial_Data_Organization_Information: Indirect_Spatial_Reference: Data were collected continuously at survey locations. Refer to self-contained netCDF files for more location information. Spatial_Reference_Information: Horizontal_Coordinate_System_Definition: Geographic: Latitude_Resolution: 1.0E-5 Longitude_Resolution: 1.0E-5 Geographic_Coordinate_Units: Decimal degrees Geodetic_Model: Horizontal_Datum_Name: World Geodetic System 1984 (WGS84) Ellipsoid_Name: WGS84 Semi-major_Axis: 6378137.0 Denominator_of_Flattening_Ratio: 298.257223563 Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: NetCDF files are self-contained and attribute information may be found in the header of the file itself. Entity_and_Attribute_Detail_Citation: 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. Distribution_Information: Distributor: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey - CMGDS Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Resource_Description: Downloadable data in netCDF format and compressed into zipped archives. Files were grouped by station (San Pablo Subtidal, Intertidal, Marsh, Corte Madera Subtidal, Intertidal, Marsh or Tidalcreek) and then by instrument type. Instrument type suffixes follow the nomenclature defined above for filenames including a two- or three-character code for the instrument type (vec, Norteks Acoustic Doppler Velocimeter; aqd, Nortek aquadopp acoustic doppler current profile; pt, RBRs bursting pressure sensor with temperature; pr, RBRs pressure sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger). Information on the files available and the data in each file is listed in the NBM_time_series_file_table.csv. Distribution_Liability: 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. Standard_Order_Process: Digital_Form: Digital_Transfer_Information: Format_Name: NetCDF Format_Version_Number: netCDF-4, CF-1.8 Format_Specification: Data are in NetCDF formats. Format_Information_Content: Downloadable zip file of time-series data in netCDF format following CF 1.8 Metadata Conventions. File download sizes range from 2.6 to 3510.418 MB. File_Decompression_Technique: WinZip or archive utility Transfer_Size: 8240.7 Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://doi.org/10.5066/P1XZFGCX Access_Instructions: Data can be downloaded using the Network_Resource_Name link and scrolling down to the Time Series Data section. Fees: None. Technical_Prerequisites: The downloadable data file has been compressed with the "zip" command and can be unzipped with Winzip or other archive utilities. To utilize these data, the user must have software capable of uncompressing the WinZip file and importing and viewing a NetCDF file. Metadata_Reference_Information: Metadata_Date: 20240806 Metadata_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: PCMSC Science Data Coordinator Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Country: United States Contact_Voice_Telephone: 831-427-7520 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001-1998