Boothbay Harbor is a town in Lincoln County, Maine, United States. The population was 2,027 at the 2020 census. It includes the neighborhoods of Mount Pisgah, and Sprucewold, the Bayville and West Boothbay Harbor villages, the Isle of Springs summer colony, and the Boothbay Harbor census-designated place. Boothbay Harbor is surrounded by the larger town of Boothbay.