The Coastal Environmental Baseline Program is a multi-year Fisheries and Oceans Canada initiative designed to work with Indigenous and local communities and other key parties to collect coastal environmental data at six pilot sites across Canada (Port of Vancouver, Port of Prince Rupert, Lower St. Lawrence Estuary, Port of Saint John, Placentia Bay, and Iqaluit). The goal of the Program is to gather local information in these areas in effort to build a better understanding of marine ecological conditions. The Maritimes region has developed a habitat classification program to align with the oceanographic interests and data needs of local communities and stakeholders, with the goal of sharing this information via open data. In 2020, a habitat survey in the lower Musquash Marine Protected Area (MPA) was undertaken to further develop this project, using an Autonomous Underwater Vehicle (AUV) equipped with high-frequency (450 kHz) side scan sonar to build a habitat map of the MPA. This dataset includes mosaicked series of sonar images (raw & position-corrected versions), covering roughly 6 km2 of marine and intertidal areas in the Musquash MPA. Doppler Velocity logs and mission-specific files for each survey are also included, along with detailed methodological documentation. These data were generated from 17 separate survey missions that were completed in August, September and October 2020.