From its source (44°57′59″N 68°38′45″W / 44.9664°N 68.6458°W / 44.9664; -68.6458 (Stillwater River source)) in Old Town, the Stillwater runs 2.3 miles (3.7 km) northwest along the northeast side of Orson Island, the site of the Penobscot Indian Reservation.

It then runs 9.2 miles (14.8 km) south along the west sides of Orson and Marsh islands, over three dammed falls.

The stream rejoins the main stem of the Penobscot in Orono.

The University of Maine campus, including the Fay Hyland Botanical Plantation, overlooks the Stillwater River near its confluence with the Penobscot River.

This article related to a river in Maine is a stub.