The U.S. Geological Survey (USGS), in cooperation with the Puerto Rico Environmental Quality Board, has compiled a series of geospatial datasets for Puerto Rico to be implemented into the USGS StreamStats application (https://streamstats.usgs.gov/ss/). These geospatial datasets, along with basin characteristics datasets for Puerto Rico published as a separate USGS data release (https://doi.org/10.5066/P9HK9SSQ), were used to delineate watersheds and develop the peak-flow and low-flow regression equations used by StreamStats. The geodatabase described herein are the seven layers: BatchPoint, huc_net_Junctions, HUCLongestFlowPath, hucpoly, Point3D, Slp1085Point, StreamLayer, streams, and Streams3D.