Gunstock Mountain stands within the watershed of the Merrimack River, which drains into the Gulf of Maine in Massachusetts. The east side of the mountain, on which the ski resorted is located, drains into Poorfarm Brook, thence into Lake Winnipesaukee, the Winnipesaukee River, and the Merrimack. The west side of the mountain drains into the Gunstock River, thence into Lake Winnipesaukee.