These datasets 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 unmanned aerial vehicles (UAV) and autonomous underwater vehicles (AUV) to provide information on water quality and/or quantity, 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. In this study, water-quality and bathymetric data were measured with an AUV during spatial surveys in the study areas near Philadelphia, PA in July 2021. Water-quality and bathymetric data were measured at various periods during the tide cycle and logged at 0.2-second intervals (5 Hz). Bathymetric data were measured using an on-board single-beam echosounder in combination with a pressure transducer. Water-quality data were measured with an EXO1 sonde built into the nose cone of the IVER3 EcoMapper AUV (YSI, 2020). The sonde was calibrated before, and checked after, each data collection trip per USGS water-quality sampling protocols (YSI, 2020; Wagner and others, 2006; Wilde, variously dated). During surveys in which the AUV was programmed to execute bank-to-bank transects, it was occasionally pushed off course by the current. Water-quality parameters measured by the AUV during the survey include: water temperature and specific conductivity (YSI sensor SKU 599870), turbidity (YSI sensor SKU 599101-01), chlorophyll and phycocyanin (YSI sensor SKU 599102-01), fluorescent dissolved organic matter (YSI sensor SKU 599104-01), and dissolved oxygen (YSI sensor SKU 599100-01). Water-quality parameters computed post survey include: salinity and density which were computed from water temperature, conductivity, vessel depth, and latitude (Jackson, 2013). Additional water-quality measurements were collected from a boat following the deployed AUV. These vertical water-quality profiles were collected with a SonTek CastAway Conductivity, Temperature, and Depth (CTD) instrument logging at 0.33-second intervals (3 Hz) (Xylem, 2017). Vertical profile measurements were made periodically by manually lowering and raising the CTD at a subset of locations while following behind the track of the AUV. Water-quality parameters measured by the CTD during the survey include water temperature, specific conductivity, and depth below water surface. The CTD also provides computed salinity, sound velocity, and water density for each measurement.