Cocheco River Watershed
Sunrise Lake is located in southern Middleton along Wolfeboro Road. The lake is 247 acres in size and most of its shoreline is developed, with the highest density of houses at its western end. A small stream drains the lake near several homes along Nicola Road. It flows south for a mile and a half, passing through forest and few small marshes and ponds. The stream crosses Silver Road, past several houses, and then joins the Cocheco River. The Cocheco River briefly passes through Middleton in the southern most point of town. It enters from New Durham, runs for about a quarter mile, and then enters Farmington.
Salmon Falls River Watershed
Jones Brook originates in Jones Brook Wildlife Management Area, east of Perkins Mountain. The brook runs east through two miles of forest, encountering little development except for a dirt road, and then joins Horn Brook. This brook flows out of a forested area east of Perkins Mountain. It runs southeast, through two miles of forest, and then passes through a culvert under Ridge Road. After crossing the road, Horn Brook runs through a series of forested wetlands and then passes several homes along Middleton Hill Road. The brook crosses this road into a partially cut forest area and then passes into Milton on its way to join the Salmon Falls River.
Branch River flows out of the mountains in northern Middleton and runs along New Portsmouth Road. As it flows east, the river passes through several small marshes. The river then passes several homes along Middleton Hill Road, and flows into Wakefield on its way to join the Salmon Falls River.