The village is centered on the former site of the mill on the east bank of the Quinebaug River, near where modern Route 205 crosses the river.
According to the United States Census Bureau, the Wauregan CDP has a total area of 0.9 square miles (2.4 km2) (or 576 acres) of which 0.9 square miles (2.3 km2) is land and 0.04 square miles (0.1 km2) (2.17%) is water.