Benthic habitat maps are an important part of ecosystem-based management as they document biotic and abiotic resources. Integrating multiple ecosystem and environmental components is challenging, and the ability to do this is highly dependent on the methodology employed. The US Coastal and Marine Ecological Classification Standard (CMECS) uses a standardized set of classifications in a hierarchal structure to create benthic habitat maps. This study used acoustic surveys and benthic samples from Pleasant Bay, Cape Cod, MA, to develop benthic habitat maps and test relationships between biotic and abiotic variables. The collected data comprise a critical baseline record of biological and physical characteristics and will inform future management decisions as well as guide future studies of coastal resources in Pleasant Bay.