Lee is in the southern section of the Berkshires, in a valley along the Housatonic River. It is west of October Mountain State Forest, with two sections of the forest in Lee. In the southwest corner of town lies a portion of Beartown State Forest, where Burgoyne Pass crosses the northern end of the mountain. Hop Brook, a marshy brook which flows from Tyringham, flows into the Housatonic in the south; other bodies of water include Laurel Lake to the north and Goose Pond to the southeast. The Appalachian Trail skirts the eastern part of town, passing through Tyringham, Becket and Washington.