According to the United States Census Bureau, the city has a total area of 6.8 square miles (18 km2), of which 6.7 square miles (17 km2) is land and 0.1 square miles (0.26 km2), or 1.47%, is water. The city is primarily within Wayne County, but a portion of the city lies in Monroe County, because the border along the Huron River follows the course of the river in 1923, the year Flat Rock was incorporated as a village. At the time, the river had two meanders, but they have since been filled in.