Mystic is located within the towns of Groton (west of the Mystic River, and also known as West Mystic) and Stonington (east of the Mystic River). It is a village and census-designated place (CDP) with no independent government because it is not a municipality. Mystic was a leading seaport of the area, located on the Mystic River, which flows into Long Island Sound, providing access to the sea. The Mystic River Bascule Bridge crosses the river in the center of the village. The name "Mystic" is derived from the Pequot term "missi-tuk", describing a large river whose waters are driven into waves by tides or wind. Mystic has three historic districts: the Mystic Bridge Historic District, Rossie Velvet Mill Historic District, and the Mystic River Historic District.

Coordinates: 41°21′15″N 71°57′59″W