Accurate benthic habitat maps are critical for resource management in coastal waters with competing uses. We used a 500 kHz phase-measuring bathymetric sonar (PMBS) and 900 kHz side-scan sonar to acquire seafloor data in estuarine and shelf environments. Grab samples and remotely operated vehicle video created geological and biological classifications for segmented maps produced by a backscatter clustering program. PMBS improves regional map resolution (<1 m), reduces the need for direct sampling, extends information on sediment–biological relationships to larger areas, and allows measurements of bedforms. Auto-segmentation was successful in environments with highly contrasting acoustic signatures and meters-scale homogeneity. Patchier communities are identifiable in PMBS data. Species preferences for sediment (i.e., tubeworm preference for sediment without shell hash) allowed us to determine potential habitat without identifying individual organisms in acoustic data. PMBS with sufficient ground-truthing offers an efficient way to map seafloor characteristics, which is critical in marine spatial planning efforts.