Goose Eye Mountain stands within the watershed of the Androscoggin River, which wraps around the Mahoosuc Range and drains into Merrymeeting Bay, the estuary of the Kennebec River, and then into the Gulf of Maine. The south side of Goose Eye drains via various streams into Sunday River and the Androscoggin. The northeast side of Goose Eye drains into Goose Eye Brook, then into Sunday River. The west side of the mountain drains via various streams into the South Branch of Stearns Brook, and then into the Androscoggin.