Fort Mountain stands within the watershed of the Penobscot River, which drains into Penobscot Bay. The south and east sides of Fort Mountain drain into Wassataquoik Stream, then into the East Branch of the Penobscot River. The northeast side of Fort Mountain drains into Annis Brook, then into Wassataquoik Stream. The northwest side of Fort drains into Little Nesowadnehunk Stream, then into Nesowadnehunk Stream, and the West Branch of the Penobscot River.