Habitat and ecosystem data used to conduct a baseline survey of coastal habitat in Lake Huron, Georgian Bay, and St. Marys River are included in this dataset. The Lake Huron Survey methodology consists of four general steps; 1) delineating the coastal ecosystem into coastal units based on water flow, ecology, and geology; 2) selecting key habitat types including wetlands, uplands (natural and anthropogenic), tributaries, and inland lakes and ponds, and the measures to assess each habitat type and the entire coastal ecosystem; 3) conducting a spatial analysis and summarizing results; and 4) sharing results.