Oceanographic time-series monitoring data of a shallow-water placement of dredged sediment in south San Francisco Bay, California, 2023-2025

Deployment A: A total of seven platforms (AN, AS, X1, X2, XL, X3, and X4) were deployed between August 14th and 15th, 2023. Platforms AN and X1 were “grate” style platforms, both were equipped with an upward looking Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter mounted onto a weighted grate placed directly on the bottom surface. AN also included an RBR logger measuring pressure and temperature. X3 consisted of a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger, as well as an RBR logger measuring pressure mounted onto was a weight-stand (single weight plate with a vertical pole). Three tripods (AS, X4, and X2) consisted of included a Nortek single point ADV (acoustic doppler velocimeter) each with a Seapoint turbidity meter. AS also had an RBR CTD (conductivity, temperature, and depth), while X2 had an addition Nortek single point acoustic doppler velocimeter with a Seapoint turbidity meter and a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger. XL, which was located at station X2, had a Sequoia Scientific Laser in-situ scattering and transmissometry (LISST 200x) particle size analyzer, an RBR Virtuoso single-channel data logger with Seapoint turbidity meter, and a Sequoia Scientific submersible acoustic backscatter sensor (LISST-ABS) logged by a Nortek Vector. The Vector's only function was to log the LISST ABS data. All turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling. XL was recovered on September 5, 2023, all other platforms were recovered on September 22, 2023.

An RDI Acoustic doppler current profiler mounted on a low-profile tripod was deployed at station X0, in the navigational channel, west of the placement area. This platform was recovered on October 11, 2023.

Deployment B: On November 2, 2023, all six stations described during Deployment A were re-occupied with the with the same instrumented platform setup. These stations included: AN, AS, X1, X2, X3, and X4. Platform XL (located at station X2) was deployed and recovered twice during deployment B and was turned at shorter intervals (approximately two-week) because of the instrumentation’s high susceptibly biofouling. The platform at X1 was runover by a vessel, sustaining some damage on December 30, data were successfully recovered from instruments on the platform, however data following the collision were removed. Platforms were recovered on January 4, 2024.

On November 2, 2023, an instrumented buoy which measure meteorological and wave parameters was deployed at a new station, MW. This platform consisted of a Nexsens CB-250 buoy equipped with an Airmar WX200 sensor to measure wind speed, buoy position and orientation, air temperature and relative barometric pressure. Directions recorded by the Nexsens buoy’s wind sensor were corrected to true north using a three-axis orientation sensor to account for motion of the buoy. Meteorological variables were averaged over a two-minute sampling interval and recorded using a Nexsens X2 data logger at 10 min intervals. The ultrasonic anemometer was located about 1.2 m above the sea surface. The buoy was recovered on August 13, 2024.

A single marsh-top station (XM) was deployed roughly 25 m back from the Bay edge. XM consisted of 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. The Seapoint turbidity meters were equipped with Zebra-Tech hydro-wipers to prevent biofouling. This platform was swapped out every 60-90 days, for a total of 4 deployments (B-E) which were always concurrent with the start/end of the other time-series platform deployment and recovery dates. The pressure sensor failed during deployment B, so only turbidity data are available during that time.

Deployment C: On January 4, 2024, stations AN, AS, X1, X2, and X3 were deployed using the same types of instrumentation as prior deployments. Station X1 was deployed with the same instrumentation as before but also included an additional RBR logger measuring pressure and temperature; X3 included an additional RBR CTD. Station X4 and X1 were deployed on January 9, 2024. XL (deployed at station X2) was recovered after two weeks and deployed again on February 8, 2025, and included an EofE ECHOLOGGER EA400 profiling altimeter. Platforms were recovered on March 6, 2024.

Deployment D: Four platforms were deployed on March 6, 2024. Station X1 consisted of a “grate” style platform again, equipped with an upward looking Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter mounted onto a weighted grate placed directly on the bottom surface. X2 consisted of a tripod equipped with two Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter, an RBR CTD, and a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger. The CTD at X2 failed, no conductivity/salinity data were published. Station X3 again consisted of a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger, an RBR CTD, as well as an RBR logger measuring pressure mounted onto was a weight-stand (single weight plate with a vertical pole). Station X4 consisted of a Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter mounted onto a tripod. All turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling. All platforms were recovered on May 1, 2024.

Deployment E: During June 18, 2024, five platforms were deployed. X1 consisted of a “grate” style platform again, equipped with an upward looking Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter, and an RBR logger measuring pressure and temperature, all mounted onto a weighted grate placed directly on the bottom surface. A new grate style platform XG was also equipped with an upward looking Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter and deployed at station X2. The CTD at X2 failed, no conductivity/salinity data were published. Station X2 also included a tripod equipped with two Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter, an RBR CTD, and a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger. Station X3 again consisted of a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger, an RBR CTD, as well as an RBR logger measuring pressure mounted onto was a weight-stand (single weight plate with a vertical pole). Station X4 again consisted of a Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter mounted onto a tripod. All turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling. Platforms were recovered on August 13, 2024.

On October 25, 2024, an instrumented buoy which measure meteorological and wave parameters was deployed again at station MW. This platform consisted of a Nexsens CB-250 buoy equipped with an Airmar WX200 sensor to measure wind speed, buoy position and orientation, air temperature and relative barometric pressure. The ultrasonic anemometer was located about 1.2 m above the sea surface. The buoy was recovered on February 10, 2025.

The raw data files from each sensor were processed and converted to netCDF using stglib python libraries, 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 1.6 were added. All times are in Coordinated Universal Time (UTC).

Data were accumulated into netCDF files. During post-processing, data collected before deployment and after recovery were removed. Data quality assurance and quality control (QAQC) was performed by inspecting all variables and replacing spurious values with the fill value. 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. Further details on 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://doi.org/10.5066/P13IQYFW) in the "Instrument configuration file" section. 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.

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. The atmospheric pressure data used for the correction were collected from NOAA station 9414523, Redwood City, CA. Gaps in the Redwood City record, which occurred during a few but not all deployment periods, were filled by interpolation data from NOAA station 9414750, Alameda, CA.

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 DMP_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.

Comparison of pressure data from the RDI ADCP at XO with the known water depth identified a scaling error later confirmed by the manufacturer. ADCP pressure data was compared with pressure data from the Nortek Aquadopp at the nearest site X1. A comparison of the mean-removed pressure from the 2 instruments resulted in a scaling factor of 1.9511 with a statistical correlation of 1.00. This scaling factor was applied to the ADCP pressure data prior to the atmospheric pressure correction.

Surface waves were sampled using a Seaview SVS-603HR wave sensor on the buoy. The sensor was configured to measure wave time-series at 4 Hz intervals during 8.5-minute bursts. Directional data were corrected to true north using the magnetic compass within the sensor and adjusted by +13 deg to account for magnetic declination at the site. Algorithms in the sensor computed bulk wave statistics and spectral information in real time were recorded to a micro-SD card in the wave sensor.

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://doi.org/10.5066/P13IQYFW. Additional information on frequency cutoffs used for the calculations can be found in the metadata of the nc data file.

Files were named with a convention that uses a 13- to 17-digit alpha-numeric code. The first three characters for this dataset are all “DMP” indicating the experiment name (Dredge Material Placement); the fourth and fifth positions represent the calendar year in which the project commenced (23, 2023); the sixth character is a letters representing the orientation of the transect the station was in (A, along-shore transect; X, cross-shore transect); the seventh character is either a letter or a number representing the station's location (N, north; S, south; M, marsh; 0-4; where 0 is the western most station and 4 is the eastern most station); 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 profiler; pt, RBRs bursting pressure sensor with temperature; pr, RBRs pressure sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger; ls, Sequoia LISST 200x; alt, EofE EchoLogger EA400 profiling altimeter; wh, RDI acoustic doppler current profiler). 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 observations, the (b-a) indicate that the file contain burst statistics/burst averaged data, while filenames with (b) indicate burst observations for bursting instruments, the (s-a) indicates the file contains wave statistics. The only exception to file naming is for station MW (the wave-met buoy), whose first five characters follow the same naming convention as other files, but 6th and 7th characters are 'MW' representing the stations name, the eighth character is a number specifying the deployment number, the ninth and tenth characters are numbers that represent the instrument position on the platform, where 01 is the top-most. The eleventh through thirteenth characters indicate the type of data (wvs, wave statistics or met, meteorological data); Information on the files available for each station and the data each file contains is listed in the DMP_time_series_file_table.csv.

The netCDF files were compressed and combined in zipped folders for each deployment (A-E, 5 total), within the zipped deployment folders are subfolders for each station. The wave-meteorological buoy data are zipped separately by deployment (2 total), the ADCP are zipped separately as well. Details on the including data type and file name for each deployment and platform can be found in the support file: DMP23_time_series_file_table.csv.