This data release provides flooding extent polygons based on wave-driven total water levels for the coral lined coast of Florida and the Commonwealth of Puerto Rico. The wave and sea-level conditions were then propagated using the XBeach over 100-m spaced shore-normal transects modified to account for base and post-storm scenarios. In situ observations following hurricanes Irma and Maria were used to create classifications of impact level to reefs where 0 = no impact, 0 - 0.05 = minor impact, 0.05 - 0.15 = moderate impact, and 0.15 - 1.00 = major impact. Categories were converted into numeric values of 0, 1, 2, and 3 that corresponded with the none, minor, moderate, and major damage category, respectively. These damage category values were interpolated using inverse distance weighting and clipped to coral and hardbottom extent. The clipped categories were converted into raster datasets for model input. Transect depth profiles were modified to reflect post-storm conditions by intersecting each profile with first a coral coverage class raster and then a reef damage raster that categorized the degree of damage from 0 (no damage) to 3 (major damage). There are 5 classes of coral cover raster described within the data set up: sand, 0-10% coral uncolonized hardbottom, 10-50% coral colonized hardbottom, 50-90% coral colonization, and more than 90% coral colonization. The greater colonization results in higher rugosity and thus hydrodynamic roughness via friction and was parameterized per van Dongeren and others (2013) and Quataert and others (2015). Where the locations along each transect were coincident with one of the damage-assessment locations, a reduction in roughness, fw and cf, and/or an increase in profile depth were applied. The changes to bathymetry and roughness were then carried on to each Xbeach model run to ascertain the change in flooding from large events due to the damage of the reefs. For each state/territory there are 8 associated flood extent shapefiles: one for each of four nearshore wave energy return periods (rp; 10-, 50-, 100-, and 500-years), and either the current scenario (base) or the post-storm scenario. These flood extents can be combined with economic, ecological, and engineering tools to provide a rigorous financial valuation of the coastal protection benefits of coral reefs of Florida and Puerto Rico. These data accompany: Storlazzi, C.D., Reguero, B.G., Viehman, T.S., Cumming, K.A., Cole, A.D., Shope, J.A., Groves, S.H., Gaido L., C., Nickel, B.A., and Beck, M.W., 2021, Rigorously valuing the impact of Hurricanes Irma and Maria on coastal hazard risks in Florida and Puerto Rico: U.S. Geological Survey Open-File Report 2021-1056, 29 p., https://doi.org/10.3133/ofr20211056.