It flows roughly south past the locality of Harris Ranch, receiving Oliver Creek and several other small, unnamed tributaries along the way.

The Chowchilla River begins in name at the point where the West and East forks converge and flows southwest to Eastman Lake.

The lake, which holds 150,000 acre⋅ft (190,000 dam3) of water from the Chowchilla, was created in 1975 by the construction of Buchanan Dam, an earth and rockfill structure which is 205 by 1,800 ft (62 by 549 m).

In the summer months, Eastman Lake is a popular boating, fishing, camping and hiking destination for residents of the Madera and Chowchilla areas.

The river has never had a defined natural outlet to the San Joaquin, as evidenced by the fact that the riverbed shrinks considerably in size as it travels west.