Black Nubble stands within the watershed of the Kennebec River, which drains into the Gulf of Maine. The east side of Black Nubble drains into Nash Stream, then into the South Branch of the Dead River, Flagstaff Lake, the Dead River and the Kennebec. The west side of Black Nubble drains into the West Branch of Nash Stream. The south end of Black Nubble drains into Orbeton Stream, then into the Sandy River, another tributary of the Kennebec River.