According to the United States Census Bureau, the town has a total area of 9.2 square miles (23.9 km2). 5.8 square miles (14.9 km2) of it is land and 3.5 square miles (9.0 km2) of it is water. The total area is 37.49% water. Boothbay Harbor is located on a peninsula in the Gulf of Maine, part of the Atlantic Ocean.
The town is crossed by state routes 27 and 96. It borders the towns of Southport to the southwest, and Boothbay to the north and east
