Belknap Mountain stands within the watershed of the Merrimack River, which drains into the Gulf of Maine in Massachusetts. The east and northeast sides of Belknap Mountain drain into Poorfarm Brook, thence into Lake Winnipesaukee, the Winnipesaukee River, and the Merrimack. The west side drains into Gunstock River, thence into Lake Winnipesaukee. The south side drains into Manning Lake, thence into Crystal Lake, the source of the Suncook River, and thence into the Merrimack River.