[2] Via the Potomac River, its waters are part of the Chesapeake Bay watershed, leading to the Atlantic Ocean.
Flowing from a hollow in Town Hill, Shawan Run feeds into the Little Cacapon at Barnes Mill.
At Higginsville on Slanesville Pike (County Route 3) near the old Vinita School, the river is fed by Crooked Run at Queens Ridge (1,322 feet (403 m) high).
At the entrance of Neals Run, the Little Cacapon is met to its east by 2,237-foot (682 m) Spring Gap Mountain and then flows beneath the Baltimore and Ohio Railroad and empties into the Potomac River.
From its source, the South Fork flows northeast toward Bell Hollow, where it meets US Route 50 and turns north through Frye's Flat towards Frenchburg.