Time-series measurements of oceanographic and water quality data collected in the Herring River, Wellfleet, Massachusetts, USA, November 2018 to November 2019

Beginning on November 12, 2018, instruments to measure time-series data of water quality, water level, currents, waves, and changes to the seabed elevations were deployed at four locations in the Herring River estuary in Wellfleet, Massachusetts. Bottom landing fiberglass platforms were deployed in the main channel on either side of a flow restriction at the Chequessett Neck bridge that limits the reach of saltier Cape Cod Bay water inland of the bridge. The platform upstream (landward) of the bridge 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 seaward (downstream) of the restriction also had a multi-parameter sonde measuring the same water quality parameters as the upstream sonde, and also included an acoustic doppler current profiler (Nortek Aquadopp) to make current profile measurements and a fast-sampling pressure logger (RBR Dwave) to measure tides and non-directional waves. On a tidal mudflat between the bridge and the seaward bottom platform, two stainless steel altimeter frames (custom built called "spyder" frames) were deployed, each with a profiling seabed altimeter (EchoLogger EA400), a turbidity sensor (WET Labs ECO-NTU), and an RBR Dwave. At approximately 3-month intervals instruments were retrieved to download data and refresh batteries, and then redeployed for the next segments. During these turnarounds the bottom landing platforms were turned around the same day by swapping instruments at time of recovery with instruments of the same type with minimal loss of data (a couple of sample intervals typically), while with the instruments on the mudflat spyder frames swapping was not an option and there was typically 2 or 3 days without data collection at those sites between deployment segments. The spyder frames were removed in January 2019 due to concerns of ice formation and were re-established in late March 2019 when the threat of ice in the area had passed. Most instruments measured and recorded parameters at 15-minute intervals during the deployments, except for the RBR Dwaves which burst sampled pressure data at a 4 Hz sampling rate for 1024 seconds, every 30 minutes. Specifics are given in the metadata of the self-describing netCDF files. Data collection ceased on October 14, 2019 for the EXO2 sonde on the landward (upstream) bottom platform due to battery depletion. The seaward bottom lander was recovered on October 23, 2019, and the 2 spyder frames on November 19, 2019, which marked the end of data collection of this dataset. More information on each of the deployment and recovery segments and data processing is given in additional process steps. Steve Suttles is the contact for this process step and subsequent process steps until otherwise noted.

Deployment A: A Nortek Aquadopp, YSI EXO2, and RBR Dwave were deployed at mooring 1121 (the seaward channel location) on a bottom lander platform on November 12, 2018. RBR Dwaves, EchoLogger EA400s, and ECO NTUs were deployed on a spyder frame at moorings 1122 (shallow flank location) and 1123 (flank deep location) on November 14, 2018. A YSI EXO2 was deployed at mooring 1120 (the landward channel location) on a bottom lander platform on November 15, 2018. On November 15, 2018, SP80 RTK receiver was used to get horizontal and vertical positions for bottom lander at mooring 1120, and altimeter spyder frames at moorings 1122 and 1123.

Recovery A part 1: The sensors and spyder frames were recovered at moorings 1122 and 1123 on January 16, 2019, due to anticipated ice in the area. Moorings 1122 and 1123 were on mudflats and the water level drops below the sensor on most low tides (twice daily).

Recovery A part 2: The sensors were recovered at mooring 1120 on February 13, 2019, and at mooring 1121 on February 15, 2019.

Deployment B part 1: A YSI EXO2 was deployed at mooring 1120 (the landward channel location) on a bottom lander platform on February 13, 2019. A Nortek Aquadopp, YSI EXO2, and RBR Dwave were deployed at mooring 1121 (the seaward channel location) on a bottom lander platform on February 15, 2019.

Deployment B part 2: Spyder frames and RBR Dwaves, EchoLogger EA400s, and ECO NTUs were deployed (re-established) at moorings 1122 (shallow flank location) and 1123 (deep flank location) on March 27, 2019.

SP80 RTK receiver was used to get horizontal and vertical positions of altimeter spyder frames at moorings 1122 (shallow flank location) and 1123 (deep flank location) on April 8, 2019.

Recovery B part 1: The EXO2 sonde was recovered at mooring 1120 on May 13, 2019, and sensors at mooring 1121 on May 16, 2019. The recovered sensors were brought back to the lab and data were downloaded and archived on a WHCMSC file server.

Recovery B part 2: RBR Dwaves, EchoLogger EA400s, and ECO NTUs were recovered at moorings 1122 and 1123 on June 19, 2019. The recovered sensors were brought back to the lab and raw data were downloaded and archived on the WHCMSC file server. SP80 RTK receiver was used to get horizontal and vertical positions of spyder frames at moorings 1122 and 1123 using average values for 15-minute occupations.

Deployment C part 1: A YSI EXO2 was deployed at mooring 1120 (landward channel location) on a bottom lander platform on May 13, 2019. A Nortek Aquadopp, YSI EXO2, and RBR Dwave were deployed at mooring 1121 (seaward channel location) on a bottom lander platform on May 16, 2019. SP80 RTK receiver was used to get horizontal and vertical positions of platform at mooring 1120 on May 13, 2019.

Deployment C part 2: RBR Dwaves, EchoLogger EA400s, and ECO NTUs were deployed on a spyder frame at moorings 1122 (shallow flank location) and 1123 (deep flank location) on June 21, 2019.

Recovery C part 1: The sensors were recovered at mooring 1120 on July 25, 2019, and at mooring 1121 on August 7, 2019. The recovered sensors were brought back to the lab and raw data were downloaded and archived on the WHCMSC file server.

Recovery C part 2: The sensors were recovered at moorings 1122 and 1123 on September 17, 2019. The recovered sensors were brought back to the lab and raw data were downloaded and archived on the WHCMSC file server.

Deployment D part 1: A YSI EXO2 was deployed at mooring 1120 (landward channel location) on a bottom lander platform on July 25, 2019. A Nortek Aquadopp, YSI EXO2, and RBR Dwave were deployed at mooring 1121 (seaward channel location) on a bottom lander platform on August 7, 2019. SP80 RTK receiver was used to get horizontal and vertical positions of platforms at moorings 1120 and 1121 on July 25, 2019, and August 7, 2019, respectively.

Deployment D part 2: RBR Dwaves, EchoLogger EA400s, and ECO NTUs were deployed on a spyder frame at moorings 1122 (shallow flank location) and 1123 (deep flank location) on September 19, 2019. SP80 RTK receiver was used to get horizontal and vertical positions of platforms at moorings 1122 and 1123 using average values for 15-minute occupations.

Recovery D part 1: The sensors were recovered at mooring 1120 on October 21, 2019, and at mooring 1121 on October 23, 2019. The recovered sensors were brought back to the lab and raw data were downloaded and archived on the WHCMSC file server.

Recovery D part 2: The sensors were recovered at moorings 1122 and 1123 on November 19, 2019. The recovered sensors were brought back to the lab and raw data were downloaded and archived on the WHCMSC file server.

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). Corrected pressure data were calculated by finding an offset with local atmospheric pressure readings when the pressure sensor was reading in air just prior to deployment and then applying the time-series of local atmospheric pressure over the course of the deployment to remove the atmospheric contribution to the deployed pressure data, leaving only the pressure due to seawater in the corrected pressure data variable (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 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 trimmig 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 D) 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 11201Aexo-a.nc, '1120' 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.

ECO-NTU data at moorings 1122 and 1123 were trimmed for times when the sensor was not fully submerged using the co-located EA400 raw altitude data. When altitude data were not in valid range ECO-NTU data were filled. A custom python script (maskntu2ea400.py) was used for this purpose.

Additional cross-reference was added to the metadata as well as updating the contacts for process steps.