The north side of Loon Mountain drains via Boyle Brook and Loon Pond Brook to the East Branch of the Pemigewasset River. To the west of the South Peak, Horner Brook drains directly to the Pemigewasset River. The southern slopes of Loon Mountain drain via Talford Brook to Eastman Brook and then into the Pemigewasset, which flows south to the Merrimack River and ultimately the Gulf of Maine.