The United States Virgin Island's (USVI) coral reefs support many economically and ecologically important fish species. Located in the Caribbean Sea, they are subject to frequent severe weather disturbances, including two category 5 hurricanes, Irma and Maria, in 2017. The overarching goal of this study was to identify reef fish community impacts following these extreme events using discontinuous survey indices. Long-term (2001–2021), in situ, fishery-independent survey data using two methods were standardized to the extent possible in two regions of the USVI, St. Thomas/St. John (STT/STJ) and St. Croix (STX). Comparable data were assessed, 73 species collected on hard- bottom habitat, to identify the number of these species with significant changes in density and/or mean length between 2-yr survey intervals over the historic baseline (2001–2015), disturbance (2017–2019), and postdisturbance (2019–2021) periods. The results varied by region: STT/STJ had no disturbance impact and STX had a significant disturbance impact. In STX, 20 species had significant changes in density in the disturbance period compared to an average of 9.7 (SD 3.8) species for the baseline period. The proportion of species with significant density increases and decreases were similar suggesting that overall disturbance impacts are nuanced. Mean length observations were less informative, likely due to survey method and sample size changes. However, in combination with density they provided useful insights into the possible causes of population change. The successful use of discontinuous survey indices to obtain meaningful biological insights has broader applications to ecosystem and fishery datasets with similar limitations.