This dataset consists of a shapefile of lines representing the bathymetric survey of Puerto Mosquito, in Isla de Vieques, Puerto Rico, on August 11, 2015. The U.S. Geological Survey, in cooperation with the Puerto Rico Environmental Quality Board, conducted a limnological study at Puerto Mosquito in Isla de Vieques 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 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)