This study investigates a way to characterize the geology and biology of the seafloor in two Marine Protected Areas on the West Florida Shelf. Characterization of benthic habitats needs to include sufficient detail to represent the complex and heterogeneous bottom types. Characterizations can be interpreted from multiple data sets and displayed as benthic habitat maps. Multibeam sonar bathymetry and backscatter provide full spatial data coverage, but interpretation of such data requires some form of ground truth (to characterize the habitat). Imagery from towed underwater video provides continuous transects of seafloor data, which provide a more efficient method than data from sediment grabs, stationary cameras, or video from slow-moving remotely-operated vehicles while a ship is on station. Two Marine Protected Areas, Steamboat Lumps and Madison-Swanson, were previously mapped by the USGS using a 95 kHz multibeam sonar system. Researchers at the University of South Florida, using a 300 kHz high-resolution multibeam sonar in 2002 and a 400 kHz high-resolution multibeam sonar in 2016, filled in the northeast triangular portion of Madison-Swanson. Bathymetry and backscatter data were compared to towed underwater-video observations. A modified version of the Coastal and Marine Ecological Classification Standard (CMECS), utilizing a scale-based hierarchy, was used for habitat characterization of video images. Identifiers from the geoform and substrate components of CMECS, as well as substrate-influencing biologic components, were characterized using still images at 15-second intervals from towed underwater video collected using the Camera-Based Assessment Survey System (C-BASS). These characterizations were then georeferenced (located in three-dimensional space) for comparison with bathymetry and backscatter data. In Steamboat Lumps, eight substrate variations were identified from video, while in Madison-Swanson 27 substrate variations were identified, including many combinations of hard and soft substrate types. Four new hard-bottom textures are identified from video in Madison-Swanson: exposed high-relief, moderate-relief, and low-relief hard bottom, as well as covered low-relief hard bottom identified by the presence of attached biota. Hard- and mixed-bottom substrate types identified from video are more heterogeneous than can be resolved from 95 kHz Kongsberg EM 1002 multibeam sonar bathymetry and beam-averaged backscatter. However, in soft bottom areas, more changes are evident in beam-averaged backscatter than are visible in video, though this may be attributed to changes in sonar settings. This does not appear to be the case with high-resolution and ultra-high resolution multibeam sonars, such as the 300 kHz Kongsberg EM 3000 and the 400 kHz Reson SeaBat 7125, which can use time-series rather than beam-averaged backscatter. Analyses of the multibeam bathymetry data indicate that 94.5% of Steamboat Lumps is “flat” (slope < 5°) versus “sloping” for the remaining area (5° < slope < 30°). Only 87% of Madison-Swanson is “flat” versus “sloping”. Both marine protected areas have very low rugosity, i.e., the surface of the seafloor is nearly planar.