This dataset consists of a shapefile of points corresponding to water depth collected for the bathymetric survey of Caño Boquerón, in Cabo Rojo, Puerto Rico, conducted on August 21, 2015. The U.S. Geological Survey, in cooperation with the Puerto Rico Environmental Quality Board, conducted a limnological study at Caño Boquerón, in Cabo Rojo to assess the principal mechanisms affecting the hydrology and water quality characteristics. The study characterized hydrologic and physical-chemical properties, sediment deposition rates, bathymetry, and biological conditions. The bathymetric survey system used for the study consisted of coupling a global positioning system (GPS) device with a water depth sounder. Established navigation lines were used to simultaneously collect the water depth and geographic location data using a bathymetric system. A bathymetric map was generated by transferring collected data into a geographic information system (GIS).