Nicole R. Buckley Kristen L. Bouska Ashley Johnson 20250930 tabular digital data https://doi.org/10.5066/P13BYQEG The U.S. Geological Survey Upper Midwest Environmental Sciences Center collected semi-continuous data from water quality and pressure sensors at four shallow locations in the impounded portion of Pool 13 of the Upper Mississippi River and one location upstream near Savanna, IL between late May and early September 2024. This dataset includes high-frequency conductivity, salinity, total dissolved solids, temperature, dissolved oxygen, and turbidity measurements every 5-minutes at five locations, with chlorophyll-a and phycocyanin concentrations being recorded at two of those locations using YSI EXO3 water quality sensors. Pressure data was recorded in bursts every 30-minutes alongside water quality at four locations using RBR virtuoso3 and Nortek Vector sensors to obtain information on local water depth and waves. Due to differing sampling frequencies, data files are grouped by sensor type. These data were collected to provide insights into the contributions from local (e.g., waves) versus upstream (e.g., turbid discharge) factors on water clarity in the shallow, impounded portion of Pool 13 of the Upper Mississippi River. The goal of this project is to produce information useful for understanding areas vulnerable to sediment resuspension, with the intention of being used to inform the selection and design of future habitat restoration initiatives that serve to improve water clarity and submerged aquatic vegetation distribution and abundance. High-frequency pressure data contained herein was collected to estimate non-directional surface wave parameters. However, these estimates have not been included in this data release to allow the users to apply their own methods for wave analysis. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. 20240523 20240919 ground condition Complete None planned -90.1936 -90.0920 42.1048 41.8972 ISO 19115 Topic Category biota None chlorophyll a phycocyanin pressure conductivity nearbed process USGS Thesaurus water temperature oxygen content (water) turbidity time series datasets river systems water quality USGS Metadata Identifier USGS:686ec0f0d4be020e5c0a6b06 None Mississippi River Navigation Pool 13 No access constraints. Please see 'Distribution Information' for details. These data are marked with a Creative Common CC0 1.0 Universal License. These data are in the public domain and do not have any use constraints. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Nicole R. Buckley U.S. Geological Survey Physical Scientist mailing and physical

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse WI 54603 608-783-6451 nbuckley@usgs.gov Funding for this work was provided by the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration program. Field work was performed in collaboration with the Iowa Department of Natural Resources. YSI EXO3 sensors were cleaned and calibrated once a month using standard methods from the EXO user manual (Item# 603789REF Revision K (ysi.com)). The compass on the Nortek Vector sensors were calibrated and the pressure offset to account for atmospheric contributions prior to the first deployment in May 2024. Field checks of water depth were occasionally done by rough comparison with the recordings on the boat's sonar between recovery and redeployment. All data points were generally within the range of expected values but occasionally exceeded the published specifications or had extreme single-point outliers. While the EXO3 sensors have the capability to apply adaptive filtering and outlier rejection, this was not possible since only a single sample is recorded every 5-minutes. All filtering and outlier detection were performed during post-processing. The removal of questionable data values is highly subjective and may result in the loss of information, disrupting further analysis and understanding. All water quality data are raw and each value was assigned a quality control flag using SeaDataNet Quality Control standards (https://www.seadatanet.org/Standards/Data-Quality-Control; 1 = good value, 2 = probably good value, 3 = probably bad value, and 4 = bad value). Suspect data were assigned with flags of 3 and 4, respectively. Details describing the quality assurance and quality control (QAQC) processes can be found in the 'Quality Control Flagging Process' subsection of the 'YSI Water Quality Data' Process Step section. Users are advised to assess data quality carefully based on their needs when using this dataset. Data were collected in a dynamic, changing physical environment. There was a flood during late June to July which resulted in elevated water levels, up to a 3-fold increase in water depth at some sites. Site locations are approximate using GPS instrumentation and likely varied several meters between deployments. Occasionally, moorings were recovered downstream of the deployed locations. While there is no certainty to know when the sensors moved from their original location, we make some suggestions based on local changes in the pressure dataset (see 'RBR Pressure Data' and 'Nortek Pressure Data' Process Steps for more details). Sensor deployment heights are approximate (see 'Field Deployment' Process Step for more details). No corrections were made to account for the variability in vertical positioning of each sensor with respect to the riverbed as some sensor platforms may have settled during the deployment or been impacted by drifting debris. Site Locations and Sensors: Data collection occurred at 5 locations in Pool 13 of the Upper Mississippi River. Deployment locations are approximate and likely varied several meters between recovery and redeployment. A YSI EXO3 was placed at Site 1 (42.10093783°N, 90.15918772°W) at a pier upstream near Savanna, IL. At Sites 3 (41.93347504°N, 90.1735187°W) and 5 (41.91781328°N, 90.1608839°W), a YSI EXO3 was coupled with an RBR virtuoso3. Sites 2 (41.93411996°N, 90.13985876°W) and 4 (41.92550987°N, 90.17183285°W) had a YSI EXO3 with additional chlorophyll and total algae sensors and was coupled with the Nortek Vector. All dates and times reported in the data files are in local Central Daylight Time (CDT). Field Deployment: YSI EXO3 water quality and RBR pressure sensors were mounted horizontally in PVC tubes and attached to cinder blocks to moor in place at the approximate site location for Sites 3 and 5. The RBR pressure sensors were mounted roughly 23 cm above the river bottom, and the YSI EXO3 sensors were between 40-50 cm above the river bottom. For Sites 2 and 4, the YSI EXO3 sensors were mounted horizontally on the sensor platform with the Nortek Vector sensors mounted vertically positioning the pressure sensor approximately 32 cm above the river bottom. 20250602 YSI Water Quality Data: All of the EXO3 sensors were equipped with conductivity (µS/cm), temperature (degrees Celsius), dissolved oxygen (% saturation; mg/L), and turbidity (NTU) sensors, with two of the sensors also containing phycocyanin (RFU; µg/L) and chlorophyll a (RFU; µg/L) sensors. Other parameters, like salinity (PSU) and total dissolved solids (mg/L), were estimated from the calibrated conductivity and temperature sensors. During the first deployment (23 May 2024) at all sites, the sensors were sampling at a 1-second frequency. This was changed to a 5-minute frequency for nearly all future deployments. Each sonde was equipped with a wiper to clean the sensor surface just prior to collection, minimizing any fouling that accumulated during the deployment. Most of the gaps in the water quality dataset are due to batteries dying while deployed. Sampling resumed after sensors were recovered on the next site visit for cleaning, battery replacement, and calibration. Below summarizes the steps taken during the post-processing for quality assurance and quality control of the datasets. The raw data were downloaded from the YSI EXO3 sensors as CSV files. Data were screened for potential outliers and sensor error in Python (Version 3.12.3). Data collected during the first deployment at a 1-second frequency at all sites (plus the second deployment for Sites 2, 4, and 5) were resampled at a 5-minute frequency to match all other deployments. Data collected while the sensor was out of the water for cleaning and calibration were excluded. Since the EXO sensors have an embedded processor that assesses sensor performance, calibrations were performed in the field and generally received a 'Good' performance score which states that the sensor was calibrated properly and should perform within the manufacturer-defined limits (see the EXO user manual for more information). A 'Warning' performance score suggests that the sensor will still perform within manufacturer-defined limits but should be observed closely as adjustments might be required in the future. A 'Bad' performance score suggests that the sensor is not performing within those defined limits and should be recalibrated. If a performance score came back as 'Warning' or 'Bad', the sensor was reset and recalibrated to improve the performance score, however, this was not always successful. While all sensors were cleaned prior to calibration, fouling accumulation may have been retained in hard-to-reach areas. During one turbidity calibration at Site 5 (performed 17 June 2024), the sensor received a 'Bad' performance score. One potential reason for poor performance could be due to gradual contamination of the deionized water used for the 0 NTU turbidity standard since all of the sensors were calibrated using the same solution. Solutions were replaced and sensors recalibrated, if possible, but the turbidity sensor retained a 'Bad' performance score for data collected between 17-19 June 2024. The calibrations of phycocyanin and chlorophyll a (both RFU and µg/L) for the first deployment (performed 21 May 2024) at Site 2, and for phycocyanin (RFU only) at Site 4 (performed 17 June 2024) received a 'Bad' performance score which could be due to the temperature sensitive nature of the rhodamine standard used. While phycocyanin, chlorophyll a, and turbidity measurements should never be negative, negative values were occasionally recorded for phycocyanin and chlorophyll a at Site 2 and 4, and turbidity at Site 5. This is likely due to differences in the sensor gain and/or condition of the standards used for those calibrations. Users should assess quality control flags carefully since the raw data contains negative values for phycocyanin, chlorophyll a, and turbidity during those windows. Quality Control Flagging Process: All data collected after a 'Good' or 'Warning' calibration were initially assigned a quality control flag of 1 (good value), indicating that these values were considered reliable. Those collected after a 'Bad' calibration were initially assigned a flag of 2 (probably good value). This flag suggests that while the values may still reflect useful trends, caution is warranted when interpreting the reported data. Any values that fell outside of the manufacturer's published range were reclassified with a quality control flag of 4 (bad value). This category includes negative measurements for phycocyanin, chlorophyll a, and turbidity, which are technically impossible, but may still provide insights into broader trends. To further ensure data integrity, point outliers were identified using a conservative, adaptive filtering approach based on the moving median absolute deviation. Each identified outlier was manually reviewed, resulting in one of two potential flags: 2 (probably good value) for those outliers that were determined to potentially represent true values, and 3 (probably bad value) for those likely not representative of actual measurements, but does fall within manufacturer published ranges. Additional Notes: Since the EXO3 at Site 4 was coupled with a Nortek Vector, a substantial change in the frame's orientation could impact the readings on the EXO3 by changing its position in the water column. Between 15:00 on 27 June and 12:00 on 1 July, there was a substantial shift in the frame orientation (see more details in the 'Nortek Pressure Data' Process Step). All associated data within that window has been flagged with a 3 as probably bad due to the substantial shift in orientation, changing the position of the EXO3 in the water column. We encourage users to assess quality control flags carefully since the removal of questionable data values is highly subjective and may result in the loss of information beneficial for other purposes. 20250602 RBR Pressure Data: The RBR pressure sensors were recovered once a month during maintenance and calibration of the attached EXO3 sensors from May to September 2024. The RBRs recorded pressure in burst intervals which recorded 4,096 samples at a frequency of 8 Hz (~8.5 minutes) and repeated every 30-minutes. The raw data files were downloaded from the RBR virtuoso3 sensors as RSK files and exported as text files using the Ruskin software. Data were screened for potential outliers and sensor error in Python (Version 3.12.3). Due to continuous recording, data collected while the sensor was out of water for cleaning and calibration of the associated EXO3 were excluded. RBR virtuoso3 sensors recorded absolute pressure (dbar; atmospheric plus water) and derived water pressure (dbar) and depth (meters) using atmospheric pressure and water density values representative of the project area. Raw atmospheric pressure along with derived water pressure and depth are reported in this data release. Pressure data from Sites 3 and 5 were compressed and combined in zipped files. Additional Notes: Due to flood levels, sensors at Site 5 were not recovered during the site visit on 16 July 2024. The sensors were recovered a few weeks later, several hundred meters downstream. While we cannot definitively say when the sensor moved downstream, we suggest that the sensor first moved from its original location around 11:30 on 5 July or around 11:30 on 7 July 2024 based on abrupt changes in the pressure sensor during that deployment window (24 June - 8 August 2024). These changes occurred during peak flood levels which introduced high flow and large debris capable of dragging sensors downstream. At Site 3, there was a noticeable difference (~0.35 dbar) between pressure readings at the recovery and redeployment of the sensors on 21 August 2024. Using the depth sensor on the boat, we confirmed that there was indeed an approximate 30 cm difference between the water depth during recovery and redeployment. This is reasonable given that these sensors are deployed at approximately the same location but likely vary several meters. Users should assess data quality carefully based on their needs when using this dataset. 20250602 Nortek Pressure Data: The Nortek Vector sensors (acoustic doppler velocimeters) were recovered once a month during maintenance and calibration of the attached EXO3 sensors from May to September 2024. The Vector sensors recorded pressure in burst intervals which recorded 9,600 samples at a frequency of 16 Hz (10-minutes) and repeated every 30-minutes. The raw data files were downloaded from the Nortek Vector as VEC files and converted to NetCDF files using a USGS Python toolbox called stglib (doi:10.5066/P13IQYFW). Data were screened for potential outliers and sensor error in Python (Version 3.12.3). Due to continuous recording, data collected while the sensor was out of water for cleaning and calibration of the associated EXO3 were excluded. Water pressure (dbar) and depth (meters) were derived using water density values representative of the project area. Raw water pressure and derived depth are reported in this data release. Pressure data from Sites 2 and 4 were compressed and combined in zipped files. Additional Notes: During the site visit on 16 July 2025, Site 4 sensors were recovered approximately 200 meters downstream. While we cannot definitively say when the sensor moved downstream, we suggest that it first moved from its original location around 17:00 on 27 June 2024 based on the abrupt change in the pressure sensor during the deployment window (24 June - 16 July 2024). Due to the size of the platform, we suspect that the movement was caused by human interference but cannot say with certainty as water levels began to increase rapidly due to flooding around this time. The Vector pressure sensors have an internal compass to track sensor stability and orientation throughout the deployment. There was a substantial shift in the sensor's orientation around 15:00 on 27 June at Site 4 that suggests the sensor had rotated, tilted forward and to the left over the course of the next 72-hours, compromising the pressure data collected during that period. The sensor returned to a near level position by 12:00 on 1 July 2024. All pressure data collected within this 93-hour window were excluded. Site 2 also saw a substantial shift in the sensor's orientation around 07:00 on 6 August 2024 which resulted in a change of roughly 25 cm. The sensor stability was not corrected until recovery and redeployment during the next site visit on 21 August 2024. All pressure data within that window was excluded. Users should assess data quality carefully based on their needs when using this dataset. 20250602 Pool13_HARP_2024_water-quality-data.csv Comma Separated Value (CSV) file containing water quality sensor data. Producer Defined Datetime Datetime (mm/dd/yyyy hh:mm) Producer Defined Local date and time of measurement Site Site identifier Producer Defined 1 5 Latitude_degN Site Latitude Producer Defined 41.91781328 42.10093783 degrees North Longitude_degE Site Longitude Producer Defined -90.1735187 -90.13985876 degrees East conductivity_uScm Conductivity Producer Defined 213.8 499.4 microSiemens per centimeter (µS/cm) conductivity_flag Quality flag for conductivity_uScm Producer Defined 1 good value Producer defined 3 probably bad value Producer defined salinity_PSU Salinity Producer Defined 0.1 0.24 practical salinity units (PSU) salinity_flag Quality flag for salinity_PSU Producer Defined 1 good value Producer defined 3 probably bad value Producer defined TDS_mgL Total dissolved solids Producer Defined 144 318 milligrams per liter (mg/L) TDS_flag Quality flag for TDS_mgL Producer Defined 1 good value Producer defined 3 probably bad value Producer defined dissolved_oxygen_%sat Dissolved oxygen Producer Defined 51.5 169.8 percent saturation dissolved_oxygen_%sat_flag Quality flag for dissolved_oxygen_%sat Producer Defined 1 good value Producer defined 3 probably bad value Producer defined dissolved_oxygen_mgL Dissolved oxygen Producer Defined 4.25 13.31 milligrams per liter (mg/L) dissolved_oxygen_mgL_flag Quality flag for dissolved_oxygen_mgL Producer Defined 1 good value Producer defined 2 probably bad value Producer defined water_temp_degC Water temperature Producer Defined 19.44 30.226 degrees Celsius water_temp_flag Quality flag for water_temp_degC Producer Defined 1 good value Producer defined 3 probably bad value Producer defined turbidity_NTU Turbidity Producer Defined -4.89 10956.33 Nephelometric Turbidity Units (NTU) turbidity_flag Quality flag for turbidity_NTU Producer Defined 1 good value Producer defined 2 probably good value Producer defined 3 probably bad value Producer defined 4 bad value Producer defined chlorophyll_RFU Chlorophyll a concentration Producer Defined << empty cell >> No Data Producer defined 0.84 205.58 Relative Fluorescence Units (RFU) chlorophyll_RFU_flag Quality flag for chlorophyll_RFU Producer Defined << empty cell >> No Data Producer defined 1 good value Producer defined 2 probably good value Producer defined 3 probably bad value Producer defined 4 bad value Producer defined chlorophyll_ugL Chlorophyll a concentration Producer Defined << empty cell >> No Data Producer defined 3.16 836.2 micrograms per liter (µg/L) chlorophyll_ugL_flag Quality flag for chlorophyll_ugL Producer Defined << empty cell >> No Data Producer defined 1 good value Producer defined 2 probably good value Producer defined 3 probably bad value Producer defined 4 bad value Producer defined phycocyanin_RFU Phycocyanin concentration Producer Defined << empty cell >> No Data Producer defined -0.53 21.07 Relative Fluorescence Units (RFU) phycocyanin_RFU_flag Quality flag for phycocyanin_RFU Producer Defined << empty cell >> No Data Producer defined 1 good value Producer defined 2 probably good value Producer defined 3 probably bad value Producer defined 4 bad value Producer defined phycocyanin_ugL Phycocyanin concentration Producer Defined << empty cell >> No Data Producer defined -0.2 22.62 micrograms per liter (µg/L) phycocyanin_ugL_flag Quality flag for phycocyanin_ugL Producer Defined << empty cell >> No Data Producer defined 1 good value Producer defined 2 probably good value Producer defined 3 probably bad value Producer defined 4 bad value Producer defined Pool13_HARP_2024_Nortek-pressure-data.csv Comma Separated Value (CSV) file containing pressure and depth-derived data. Producer Defined Datetime Datetime (mm/dd/yyyy hh:mm) Producer Defined Local date and time of measurement Site Site identifier Producer Defined 2 4 Latitude_degN Site Latitude Producer Defined 41.92551 41.93412 degrees North Longitude_degE Site Longitude Producer Defined -90.171833 -90.139859 degrees East water_pressure_db Water pressure Producer Defined 0.0 3.009 decibar (db) depth_m Depth Producer Defined 0.0 3.080 meters (m) Pool13_HARP_2024_RBR-pressure-data.csv Comma Separated Value (CSV) file containing pressure and depth-derived data. Producer Defined Datetime Datetime (mm/dd/yyyy hh:mm) Producer Defined Local date and time of measurement Site Site identifier Producer Defined 3 5 Latitude_degN Site Latitude Producer Defined 41.917813 41.933475 degrees North Longitude_degE Site Longitude Producer Defined -90.173519 -90.160884 degrees East absolute_pressure_db Absolute pressure Producer Defined 10.45026 12.84723 decibar (db) water_pressure_db Water pressure Producer Defined 0.318 2.715 decibar (db) depth_m Water depth Producer Defined 0.325 2.776 meters (m) U.S. Geological Survey - ScienceBase mailing address

Denver Federal Center

Building 810

Mail Stop 302

Denver CO 80225 1-888-275-8747 sciencebase@usgs.gov 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 for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Digital Data https://doi.org/10.5066/P13BYQEG None Due to the file size, the downloadable pressure data files (“Pool13_HARP_2024_Nortek-pressure-data” and “Pool13_HARP_2024_RBR-pressure-data”) have 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 the CSV file (e.g., Python, R, MATLAB). 20250930 Nicole R. Buckley U.S. Geological Survey Physical Scientist mailing and physical

2630 Fanta Reed Road

La Crosse WI 54603 608-783-6451 nbuckley@usgs.gov FGDC Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998