The U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center conducted research to quantify bathymetric changes along the Florida Reef Tract (FRT) from Miami to Marquesas Keys within a 939.4 square-kilometer area between 2016 and 2019. USGS staff used light detection and ranging (lidar)-derived data acquired by the National Oceanic and Atmospheric Administration (NOAA) during two separate lidar surveys. The first is dataset is referenced as "2016 lidar" data and was collected between July 21, 2016 and February 20, 2017 (NOAA, 2017a-c and 2018) and the second is denoted as "2019 lidar" data and was collected between November 20, 2018 and March 23, 2019 (NOAA, 2020). The 2016 and 2019 NOAA lidar datasets were used to assess changes in elevation and structure that occurred during this period along the FRT. An elevation change analysis between the 2016 and 2019 lidar data was performed to quantify and map impacts to seafloor elevation and determine elevation and volume change statistics for individual habitats found within the FRT. Data were collected under Florida Keys National Marine Sanctuary permit FKNMS-2016-068.