This report describes the development and assessment of shallow (0-40 m) benthic habitat maps for Fish Bay, Coral Bay and the St. Thomas East End Reserve (STEER) in the U.S. Virgin Islands. The objective of this effort, conducted by NOAA’s National Centers for Coastal Ocean Science in partnership with the Nature Conservancy (TNC), the U.S. National Park Service (NPS) and the Virgin Islands Department of Planning and Natural Resources (DPNR), was to provide spatially-explicit information describing the benthic habitat types and live coral cover present in these three locations. This habitat information will support the development of local action strategies for coral reef conservation in each of these places, providing roadmaps to address key issues and remedy specific threats to coral reefs. The three habitat maps, generated using a combination of semi-automated classification and visual interpretation techniques, represent the first digital maps that describe nearly 100% of the seafloor in these areas. This effort also marks the first time that high resolution imagery describing seafloor depth was collected in these locations.