According to the United States Census Bureau, the CDP has a total area of , of which is land and , or 10.6%, is water. The village is on the east and west bank of the estuary of the Mystic River. Mason's Island (Pequot language: Chippachaug) fills the south end of the estuary. Most of the bedrock of Mystic is "gneissic, crystalline terrane extending from eastern Massachusetts through western Rhode Island and across southeastern Connecticut north of Long Island Sound," according to geologist Richard Goldsmith.
According to the United States Census Bureau, the CDP has a total area of , of which is land and , or 10.6%, is water. The village is on the east and west bank of the estuary of the Mystic River. Mason's Island (Pequot language: Chippachaug) fills the south end of the estuary. Most of the bedrock of Mystic is "gneissic, crystalline terrane extending from eastern Massachusetts through western Rhode Island and across southeastern Connecticut north of Long Island Sound," according to geologist Richard Goldsmith.