These data were collected 2011-2012 from select locations on St. Thomas, St. Croix, and St. John (U.S. VI) in order to 1) to spatially characterize and monitor the distribution, abundance, and size of both reef fishes and macro-invertebrates (conch, lobster, Diadema); 2) to relate this information to in situ data collected on water quality and associated habitat parameters; 3) to use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting; 4) to establish the efficacy of those management decisions; 5) to work with the National Coral Reef Monitoring Program to develop data collection standards and easily implemented methodologies for transference to other agencies and to work toward standardizing data collection throughout the U.S. states and territories; and to 6) conduct a baseline characterization of fish and benthic communities. This work was variously conducted in collaboration with the Virgin Islands Department of Planning and Natural Resources, the Nature Conservancy, the University of Miami, the U.S. Department of Interior National Park Service and the University of the Virgin Islands. These data include benthic habitat data (benthic coverage type, species, percent cover), reef fish survey data (habitat and species), and macroinvertebrate counts with included metadata in FGDC (Federal Geographic Data Committee) format. Data are in ASCII, Microsoft EXCEL, and .csv format and are in individual subfolders by year and island location.