Underwater video and photographs were acquired between 28 July 2016 and 9 August 2016 at nearly 600 sites throughout the lagoon to document the presence and percent-cover of benthic substrate and cover types. Two sets of independent data were collected, one for Ground Validation (n = 292) and the other for Accuracy Assessment (n = 273). Abundances for five substrate and seven cover types were estimated to the nearest 10% in real time. These presence/absence data were used to create and evaluate the accuracy of the habitat predictions and map in Saipan Lagoon.