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This paper, using pre-storm, immediate post-storm and recovery data, quantifies seafloor elevation and volume change within the Looe Key Reef system of the Florida Keys Reef Tract over a 2.5-year period from 2016–2019 and to examine impacts from category-4 Hurricane Irma and post-storm re-equilibration of seafloor sediments. The study highlights the need to data collected over seasonal and annual time periods to improve characterization and understanding of short-term (event-driven, seasonal, interannual) and long-term (decadal to multi-decadal) rates and processes of seafloor change and help guide benthic habitat post-storm recovery and restoration efforts in topographically complex coral reef systems.