Shallow coral reef and seamount-based ecosystems associated with Pacific islands and atolls host a high and abundant biodiversity, yet many of the ecosystems are threatened by a range of climatic, oceanographic, and anthropogenic stresses. In these types of environments, the morphology and composition of the seabed have been shown to be useful proxies/surrogates for the distribution and abundance of benthic organisms, as well as the other organisms and communities that depend on them. We developed classification approaches for substrate mapping in coral reef and deeper-water environments (0–500 m) around the main Hawaiian Islands (MHI) based on multibeam echosounder bathymetry and backscatter, utilizing several key morphological variables together with the backscatter data in an unsupervised classification.