These data sets were created in support of the U.S. Geological Survey's (USGS) Next Generation Water Observing System (NGWOS) for the Delaware River Basin pilot study (Eberts, Wagner, and Woodside, 2019). The NGWOS utilizes real-time data, improved computational capabilities, and new technologies such as the rapid deployment of unmanned aerial vehicle's (UAV) and autonomous underwater vehicle's (AUV) to provide information on water quantity and quality, in more locations, quickly and efficiently (Eberts, Wagner, and Woodside, 2019). Combined with advanced modeling applications, the NGWOS will be an important tool for water-resource managers and emergency management. Water-quality and bathymetric data were measured with an Autonomous Underwater Vehicle (AUV) during spatial surveys in the study areas near Philadelphia, Chester, and Fort Mifflin, PA in December 2019. Water-quality and bathymetric data were measured and logged at 1-second intervals. Bathymetric data were measured using an on-board depth sounder and pressure transducer. Water-quality data were measured with a YSI 6600 V2 sonde mounted in the nose cone of the IVER2 EcoMapper AUV. The sonde was calibrated before, and checked after, each data collection trip per USGS water-quality sampling protocols (YSI, 2012; Wagner and others, 2006; Wilde, variously dated). See processing steps for additional information related to calibration and checks. Data were measured at various periods of the tide cycle and the AUV was occasionally pushed off course by current, particularly when attempting a bank-to-bank transect mission. Water-quality parameters measured by the AUV during the survey include: specific conductivity (microSiemens per centimeter at 25 degrees Celsius; YSI sensor 6560), salinity (parts per thousand; computed from conductivity), water temperature (degrees Celsius; YSI sensor 6560), phycocyanin as fluorescence (relative fluorescence units (RFU); YSI sensor 6131), total chlorophyll as fluorescence (RFU; YSI sensor 6025), dissolved oxygen (milligrams per liter; YSI optical sensor 6150), pH (standard units; YSI sensor FR 6589), and turbidity (formazin nephelometric units; YSI sensor 6136) (YSI, 2012 and 2019). Eberts, S.M., Wagner, C.R., and Woodside, M.D., 2019, Water priorities for the Nation—The U.S. Geological Survey Next Generation Water Observing System: U.S. Geological Survey Fact Sheet 2019–3046, 2 p., https://doi.org/10.3133/fs20193046. Wagner, R.J., Boulger, R.W., Oblinger, C.J., and Smith, B.A., 2006, Guidelines and standard procedures for continuous water-quality monitors—Station operation, record computation, and data reporting: U.S. Geological Survey Techniques and Methods, book 1, chap. D3, 83 p. [Also available at https://doi.org/10.3133/tm1D3.] Wilde, F.D., ed., chapter sections variously dated, Field measurements: U.S. Geological Survey Techniques of Water-Resources Investigations, book 9, chap. A6; accessed May 13, 2020, at http://pubs.water.usgs.gov/twri9A6/ YSI, Inc., 2012, 6-series multiparameter water quality sondes user manual: YSI, Incorporated, accessed May 12, 2020, at https://www.ysi.com/File%20Library/Documents/Manuals/069300-YSI-6-Series-Manual-RevJ.pdf