These remotely sensed, geographically referenced elevation measurements of Lidar-derived submerged topography were produced as a collaborative effort between the U.S. Geological Survey (USGS), Florida Integrated Science Center (FISC), St. Petersburg, FL; the National Park Service (NPS), South Florida-Caribbean Network, Miami, FL; and the National Aeronautics and Space Administration (NASA), Wallops Flight Facility, VA. This project provides highly detailed and accurate bathymetric datasets of a portion of the U.S. Virgin Islands, acquired on April 21, 23, and 30, May 2, and June 14 and 17, 2003. The datasets are made available for use as a management tool to research scientists and natural resource managers. An innovative airborne Lidar instrument originally developed at the NASA Wallops Flight Facility, and known as the Experimental Advanced Airborne Research Lidar (EAARL), was used during data acquisition. The EAARL system is a raster-scanning, waveform-resolving, green-wavelength (532-nanometer) Lidar designed to map near-shore bathymetry, topography, and vegetation structure simultaneously. The EAARL sensor suite includes the raster-scanning, water-penetrating full-waveform adaptive Lidar, a down-looking red-green-blue (RGB) digital camera, a high-resolution multi-spectral color infrared (CIR) camera, two precision dual-frequency kinematic carrier-phase GPS receivers, and an integrated miniature digital inertial measurement unit, which provide for submeter georeferencing of each laser sample. The nominal EAARL platform is a twin-engine Cessna 310 aircraft, but the instrument may be deployed on a range of light aircraft. A single pilot, a Lidar operator, and a data analyst constitute the crew for most survey operations. This sensor has the potential to make significant contributions in measuring sub-aerial and submarine coastal topography within cross-environmental surveys. Elevation measurements were collected over the survey area using the EAARL system, and the resulting data were then processed using the Airborne Lidar Processing System (ALPS), a custom-built processing system developed in a NASA-USGS collaboration. ALPS supports the exploration and processing of Lidar data in an interactive or batch mode. Modules for presurvey flight line definition, flight path plotting, Lidar raster and waveform investigation, and digital camera image playback have been developed. Processing algorithms have been developed to extract the range to the first and last significant return within each waveform. ALPS is used routinely to create maps that represent submerged or first surface topography. Specialized filtering algorithms have been implemented to determine the 'bare earth' under vegetation from a point cloud of last return elevations.