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 Key West within a 939.4 square-kilometer area. USGS staff calculated changes in seafloor elevation and volume from 2016 to 2019 using light detection and ranging (lidar)-derived digital elevation models (DEMs) acquired by the National Oceanic and Atmospheric Administration (NOAA) in 2016, 2017 and 2019. Most of the elevation data from the 2016/2017 time period was collected during 2016, and as an abbreviated naming convention, we refer to this time period as 2016. Elevation and volume change statistics were determined for 17 habitat types found within the study area along the FRT. This data release contains elevation-change point data, elevation-change triangulated irregular network (TIN) surface models, lidar digital elevation models (DEMs) and habitat polygons used in this analysis, and elevation and volume change statistics for the geographic extent of this work. The full geographic extent of this analysis was subdivided into 5 blocks as indicated in Figure 1. Data were collected under Florida Keys National Marine Sanctuary permit FKNMS-2016-068.