It is situated at the northern end of the harbor of the same name, an arm on the east side of Frenchman Bay.

Maine State Route 186 is the primary road through the community.

To the north, the CDP includes the small community of Gerrishville.

The CDP is bordered to the west by Frenchman Bay and extends south to include all of Grindstone Neck between Frenchman Bay and the Winter Harbor inlet.

According to the United States Census Bureau, the Winter Harbor CDP has an area of 2.2 square miles (5.6 km2), all land.