The original National Aeronautics and Space Administration (NASA) Experimental Advanced Airborne Research Lidar (EAARL), was extensively modified to increase the spatial sampling density and improve performance in water ranging from 3–44 m. The new (EAARL-B) sensor features a 300% increase in spatial density, which was achieved by optically splitting each laser pulse into 3 pulses spatially separated by 1.6 m along the flight track and 2.0 m across-track on the water surface when flown at a nominal altitude of 300 m. Improved depth capability was achieved by increasing the total peak laser power by a factor of 10, and incorporating a new “deep-water” receiver, optimized to exclusively receive refracted and scattered light from deeper water (15–44 m). Two clear-water missions were conducted to determine the EAARL-B depth calibration coefficients. The calibration mission was conducted over the U.S. Navy’s South Florida Testing Facility (SFTF), an established lidar calibration range located in the coastal waters southeast of Fort Lauderdale, Florida. A second mission was conducted over Lang Bank, St. Croix, U.S. Virgin Islands. The EAARL-B survey was spatially and temporally coincident with multibeam sonar surveys conducted by the National Oceanic and Atmospheric Administration (NOAA) ship Nancy Foster. The NOAA depth data range from 10–100 m, whereas the EAARL-B captured data from 0–41 m. Coefficients derived from the SFTF calibration mission were used to correct the EAARL-B data from both missions. The resulting calibrated EAARL-B data were then compared with the original reference dataset, a jet-ski-based single beam sonar dataset from the SFTF site, and the deeper NOAA data from St. Croix. Additionally, EAARL-B depth accuracy was evaluated by comparing the depth results to International Hydrographic Organization (IHO) standards. Results show good agreement between the calibrated EAARL-B data and all three reference datasets, with 95% confidence levels well within the maximum allowable total vertical uncertainty for IHO Order 1 surveys.