Milford Fish Hatchery is bounded to the north by North River Road and to the south by the Souhegan River. The property slopes southward to, and is bisected by, Purgatory Brook. A large wetland complex connects Purgatory brook and the Souhegan River about a half mile before the brook empties into the river. The hatchery operation covers 10.5 acres, approximately 48 acres are wooded (mostly pine and some maple), 14 acres are a mix of brush and shrubland along the Souhegan River, and the remaining acreage is in agricultural fields that are farmed by a local farmer in cooperation with Fish and Game.