It drains parts of Archuleta, Hinsdale, and Mineral counties along a mainstem length of about 40 miles (64 km).

The Middle Fork, larger of the two, rises in a bowl-shaped valley in the San Juan National Forest.

The East Fork starts at a small unnamed lake in the Rio Grande National Forest and flows southwest for about 11 miles (18 km).

It receives Heffin and Yellowjacket Creeks, both from the right, and at the confluence with the latter, flows past the town of Piedra and crosses under U.S. Highway 160.

Its confluence with the San Juan River, inside Navajo State Park, is drowned under the waters of the reservoir.