Time-series measurements of oceanographic and water quality data collected at Thompsons Beach and Stone Harbor, New Jersey, USA, September 2018 to September 2019 and March 2022 to May 2023

Beginning in September 2018, instruments to measure time-series data of water quality, water level, currents, and waves were deployed at two locations in the main marsh channel northeast of Thompsons Beach, NJ and two locations in a marsh channel in southwestern Stone Harbor, NJ. On September 18, 2018, a bottom landing fiberglass platform was used for one of the instrumented platforms in the marsh channel at Stone Harbor. This platform had a multi-parameter water quality sonde (YSI EXO2) that measured pressure, salinity, water temperature, turbidity, oxygen, fluorescent dissolved organic matter (fDom), Chlorophyll, and blue green algae fluorescence. The platform also had a fast-sampling pressure logger (RBR Dwave) to measure tides and non-directional waves. On September 19, 2018, two instrumented bottom landing fiberglass platforms were deployed in the marsh channel at the Thompsons Beach site. The platform further south (seaward), had an acoustic Doppler current profiler (Nortek Aquadopp) that measured water velocity, pressure, and temperature. The platform further north (landward) had a multi-parameter water quality sonde (YSI EXO2) and a fast-sampling pressure logger (RBR Dwave) measuring the same parameters as the platform in the marsh channel at Stone Harbor. On October 10, 2018, a second instrumented bottom landing fiberglass platform was deployed further southwest in the marsh channel in Stone Harbor, NJ (closer to the creek mouth). This platform had an acoustic Doppler current profiler (Sontek IQ Plus) to measure water level, water velocity, and estimate flow/discharge. At approximately 2.5-month intervals, the platforms were recovered and the instruments were removed to download the data. New instruments were attached to the platforms and redeployed the same day resulting in minimal loss of data. On September 24 and 25, 2019, all instruments and platforms were recovered and removed from all 4 marsh channel sites. Data collection was paused until March 22, 2022, when all instrumentation was redeployed at the same marsh channel sites. The instrument platforms deployed at the Stone Harbor site in March 2022 were identical to those deployed in September 2018; however, the grated platforms were replaced with fence posts driven into the seabed allowing instrument mounts to be attached higher above the channel bed to avoid sand burial of the sensors. All instruments measured and recorded parameters at 15-minute intervals during the deployments, except for the RBR Dwaves. The RBR Dwaves burst sampled pressure data at 4 Hz for 1024 seconds, every 30 minutes in 2018-2019 and sampled continuously at 4 Hz in 2022-2023. Specifics are given in the metadata of the netCDF files. In February 14, 2023, all instruments and platforms were recovered and removed, except the seaward platform at Thompsons Beach, which was not recoverable due to marsh grass covering the platform. A second attempt was made to recover the seaward platform at Thompsons Beach in March 28 and 29, 2023; however, this attempt was unsuccessful as well. Finally, the platform was recovered on May 16, 2023, which marked the end of the data collection of this dataset. More information on each of the deployment and recovery segments and data processing is given in additional process steps.

Deployment 1116A, 1118AB, and 1119A: On September 18, 2018, a YSI EXO2 and RBR Dwave were deployed at mooring 1116A (the northeast site at the Stone Harbor marsh channel) on a bottom lander platform. An SP80 RTK receiver was used to get horizontal and vertical positions of the platform. On September 19, 2018, a YSI EXO2, and RBR Dwave were deployed at mooring 1119A (the landward site at the Thompsons Beach marsh channel) on a bottom lander platform and a Nortek Aquadopp was deployed at mooring 1118AB (the seaward site at the Thompsons Beach marsh channel). Steve Suttles is the contact for this process step and subsequent process steps until otherwise noted.

Deployment 1115A: On October 10, 2018, a Sontek IQ Plus was deployed at mooring 1115A (the southwest site in the Stone Harbor marsh channel) on a bottom lander platform. An SP80 RTK receiver was used to get the horizontal and vertical positions of platform as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations.

Recovery 1115A, 1116A, and 1119A: On December 4, 2018, the YSI EXO2 and RBR Dwave were recovered at mooring 1116A.The Sontek IQ measurements at 1115A were stopped and the data downloaded. On December 5, 2018, the YSI EXO2 and RBR Dwave were recovered at mooring 1119A. Data was downloaded from all recovered instruments and archived on a WHCMSC (Woods Hole Coastal and Marine Science Center) file server.

Deployment 1115B, 1116B, and 1119B: On December 4, 2018, the Sontek IQ Plus was configured to continue collecting data at mooring 1115B. A YSI EXO2 and RBR Dwave were deployed at mooring 1116B on a bottom lander platform. An SP80 RTK receiver was used to get the horizontal and vertical positions of 1115B and 1116B platforms, as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations. On December 5, 2018, a YSI EXO2 and RBR Dwave were deployed at 1119B.

Recovery 1115B, 1116B, and 1118AB: On February 26, 2019, the Nortek Aquadopp was recovered from mooring 1118AB. An attempt was made to retrieve 1119B; however, was not successful and was left deployed. On February 27, 2019, the YSI EXO2 and RBR Dwave were recovered from mooring 1116B. The Sontek IQ data collection was stopped and the data were downloaded at mooring 1115B. Data were downloaded from all recovered instruments and archived on a WHCMSC file server.

Deployment 1115C, 1116C, 1118CD: On February 26, 2019, the Nortek Aquadopp was deployed at 1118CD. Instruments for 1119C were not deployed because the 1119B platform recovery was unsuccessful. On February 27, 2019, the Sontek IQ Plus was configured to continue collecting data at mooring 1115C. A YSI EXO2 and RBR Dwave were deployed at mooring 1116C on a bottom lander platform. An SP80 RTK receiver was used to get the horizontal and vertical positions of the 1115C and 1116C platforms, as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations.

Deployment 1119D: On April 24, 2019, a YSI EXO2 and RBR Dwave were deployed at mooring 1119D. Another unsuccessful attempt was made to recover 1119B, so the platform remained deployed. 1119D was deployed about 25m further west than 1119B to avoid instrumentation damage at 1119B.

Recovery 1115C and 1116C: On April 25, 2019, the YSI EXO2 and RBR Dwave were recovered from mooring 1116C. The Sontek IQ measurements at mooring 1115C were stopped and the data downloaded. The data were downloaded from all recovered instruments and archived on a WHCMSC file server.

Deployment 1115D and 1116D: On April 25, 2019, the Sontek IQ Plus was configured to continue collecting data at mooring 1115D. A YSI EXO2 and RBR Dwave were deployed at mooring 1116D on a bottom lander platform. An SP80 RTK receiver was used to get the horizontal and vertical positions of 1115D and 1116D platforms as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations.

Recovery 1119B: On June 13, 2019, the YSI EXO2 and RBR Dwave were recovered from mooring 1119B using USGS divers. Data was downloaded from all recovered instruments and archived on a WHCMSC file server.

Recovery 1115D, 1116D, 1118CD, 1119D: On July 16, 2019, the YSI EXO2 and RBR Dwave were recovered from mooring 1116D. The Sontek IQ Plus measurements at mooring 1115D were stopped and data downloaded. On July 17, 2019, the YSI EXO2 and RBR Dwave were recovered from mooring 1119D and the Nortek Aquadopp was recovered from mooring 1118CD. Data was downloaded from all recovered instruments and archived on a WHCMSC file server.

Deployment 1115E, 1116E, 1118E, and 1119E: On July 16, 2019, the Sontek IQ Plus was configured to continue collecting data at mooring 1115E. A YSI EXO2 and RBR Dwave were deployed at mooring 1116E on a bottom lander platform. An SP80 RTK receiver was used to get the horizontal and vertical positions of 1115E and 1116E platforms as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations. On July 17, 2019, the Nortek Aquadopp was deployed at 1118E and a YSI EXO2 and RBR Dwave at mooring 1119E.

Recovery 1115E, 1116E, 1118E, and 1119E: On September 24, 2019, all sensors were recovered from 1118E and 1119E at Thompsons Beach. On September 25, 2019, all sensors were recovered from 1115E and 1116E at Stone Harbor. The recovered sensors were brought back to the lab and raw data were downloaded and archived on the WHCMSC file server.

Deployment 11150A, 11151A, 11152AB, and 11153A: On March 22, 2022, the Sontek IQ Plus was deployed on a fiberglass grate (parallel to bed, like bottom landing grated platforms) mounted to a fence post for mooring 11150A (the southwest site at Stone Harbor marsh channel). A YSI EXO2 and RBR Dwave were deployed at mooring 1151A (the northeast site at Stone Harbor marsh channel) on a fence post mount. A SP80 RTK receiver was used to get horizontal and vertical positions of 1150A and 1151A platforms as well as a cross-sectional survey of marsh channel for Sontek IQ Plus flow calculations. A Nortek Aquadopp was deployed at 1152AB (seaward site at marsh channel northeast of Thompsons Beach) and a YSI EXO2 and RBR Dwave at mooring 1153A (landward site at marsh channel northeast of Thompsons Beach) both using bottom lander platforms. Robert Bales is the contact for this process step and subsequent process steps until otherwise noted.

Recovery 1150A, 1151A, 1153A: On June 06, 2022, the YSI EXO2 and RBR Dwave were recovered from mooring 1153A. On June 7, 2022, the YSI EXO2 and RBR Dwave were recovered from mooring 1151A. Technical issues occurred while attempting to communicate with the Sontek IQ Plus at mooring 1150A. The Sontek IQ Plus was removed from mooring 1150A and taken offsite for troubleshooting and the power/comms cable was replaced. Data was downloaded from all recovered instruments and archived on a WHCMSC file server.

Deployment 1150B, 1151B, 1153B: On June 6, 2022, a YSI EXO2 and RBR Dwave were deployed at mooring 1153B. On June 7, 2023, a YSI EXO2 and RBR Dwave were deployed at 1151B. On June 8, 2022, the Sontek IQ Plus was redeployed at 1150B after troubleshooting was completed. An SP80 RTK receiver was used to get the horizontal and vertical positions of 1150B and 1151B platforms as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations.

Recovery 1150B, 1151B, 1152AB, and 1153B: On August 11, 2022, the YSI EXO2 and RBR Dwave were recovered from mooring 1153B. The attempt to recover 1152AB was unsuccessful. On August 12, 2022, the YSI EXO2 and RBR Dwave were recovered from mooring 1151B and data collection was stopped and data downloaded for the Sontek IQ Plus at mooring 1150B. On August 13, 2022 the Nortek Aquadopp was recovered from 1152AB. Data was downloaded from all recovered instruments and archived on a WHCMSC file server.

Deployment 1150C, 1151C, 1152C, and 1153C: On August 11, 2022, a YSI EXO2 and RBR Dwave were deployed for mooring 1153C on a bottom landing platform. On August 12, 2022, the Sontek IQ Plus was configured to continue collecting data for mooring 1150C and a YSI EXO2 and RBR Dwave were deployed for mooring 1151C. An SP80 RTK receiver was used to get the horizontal and vertical positions of 1150C and 1151C moorings as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations. On August 13, 2022, a Nortek Aquadopp was deployed at 1152C.

Recovery 1150C, 1151C, 1152C, and 1153C: On September 26, 2022, the YSI EXO2 and RBR Dwave were recovered from mooring 1153C and a Nortek Aquadopp was recovered for mooring 1152C. On September 28, 2022, the YSI EXO2 and RBR Dwave were recovered from mooring 1151C. The Sontek IQ Plus measurements were stopped and data were downloaded at mooring 1150C. Data was downloaded from all recovered instruments and archived on a WHCMSC file server.

Deployment 1150D, 1151D, 1152DE, and 1153D: On September 26, 2022, a Nortek Aquadopp was deployed at 1152DE and a YSI EXO2 and RBR Dwave at mooring 1153D. On September 28, 2022, the Sontek IQ Plus was configured to collect data at mooring 1150D and a YSI EXO2 and RBR Dwave were deployed at mooring 1151D. An SP80 RTK receiver was used to get the horizontal and vertical positions of 1150D and 1151D platforms as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations.

Recovery 1150D, 1151D, and 1153D: On December 6, 2022, the YSI EXO2 and RBR Dwave were recovered from mooring 1151D. The Sontek IQ Plus measurements were stopped and data were downloaded at mooring 1150D. On December 8, 2022, the YSI EXO2 and RBR Dwave were recovered for mooring 1153D. Data was downloaded from all recovered instruments and archived on a WHCMSC file server.

Deployment 1150E, 1151E, and 1153E: On December 6, 2022, the Sontek IQ Plus was configured to collect data at mooring 1150E and a YSI EXO2 and RBR Dwave were deployed at mooring 1151E. An SP80 RTK receiver was used to get the horizontal and vertical positions of 1150E and 1151E platforms as well as a cross-sectional survey of the marsh channel for Sontek IQ Plus flow calculations. On December 8, 2022, a YSI EXO2 and RBR Dwave were deployed at mooring 1153E.

Recovery 1150E, 1151E, and 1153E: On February 14, 2023, all sensors and equipment were recovered from 1150E, 1151E, and 1153E. An attempt was made to recover 1152DE, but due to suspected plant material covering the platform, the recovery was unsuccessful. The recovered sensors were brought back to the lab and raw data were downloaded and archived on the WHCMSC file server.

Recovery 1152DE: On March 22, 2023, another failed attempt to recover 1152DE was made. On May 16, 2023, the Nortek Aquadopp and all mooring equipment was recovered at 1152DE which marked the end of the data collection of this dataset. The recovered sensor was brought back to the lab and raw data were downloaded and archived on the WHCMSC file server.

Flow data from the raw the Sontek IQ Plus datasets were calculated by inputting marsh channel cross-section measurements in the SonTek IQ: Intelligent Flow v3.0 software and reexported in .mat format. The channel cross-section data was collected from SP80 RTK surveys on the day of each mooring segment deployment.

Flow data from the Sontek IQ Plus datasets were reversed using SonTek IQ: Intelligent Flow v3.0 software and reexported in .mat format.

The raw data files from each sensor 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 1.6 were added. All times are in Coordinated Universal Time (UTC). For all pressure sensors except the Sontek IQ, 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). The pressure sensor from the Sontek IQ Plus was corrected internally (by the IQ firmware) to eliminate atmospheric pressure using the vertical beam (beam 5). Data quality assurance and quality control (QAQC) was performed by inspecting all variables and replacing spurious values with the fill value. 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. The netCDF files are named using the convention ####XYZZZ-a.nc where '####' is the mooring number, 'X' is the position on the mooring of the sensor with 1 being closest to the surface and 3 being the most submerged, 'Y' is a letter (A through E) corresponding to the sequential deployment at each mooring location, and 'ZZZ' is an abbreviation for the instrument that was deployed. For example, in the file 11531Aexo-a.nc, '1153' is the mooring number, '1' is the position of the sensor on the mooring, 'A' indicates the first deployment, and 'exo' refers to the YSI EXO2 sensor. If the instrument was left in the field for the duration of multiple deployments, ‘Y’ will include two letters that correspond to the deployments. For example, 11521ABaqd-a.nc.