The Coastal and Marine Ecological Classification Standard (CMECS) was applied to four portions of Acadia National Park, USA, focusing on intertidal rocky and tidal flat habitats. Side-scan sonar coupled with multi-phase echo sounder bathymetry are the primary data sources used to map the seafloor, coupled with underwater video imagery and surface grab samples for grain size and macrofaunal analysis. The CMECS Substrate, Geoform, and Biotic components were effective in describing the study areas. However, integrating the CMECS components to define Biotopes was more challenging due to the limited number of grab samples available and because the dominant species within a given map unit is largely inconsistent. While Biotopes ultimately could not be defined in this study, working within the CMECS framework to create statistically significant biotopes revealed the complexity of these study areas that may otherwise have been overlooked. This study demonstrates the effectiveness of the CMECS classification, including the framework’s ability to be flexible in communicating information.