The Eel River originates on the southern flank of Bald Mountain in northeastern Mendocino County. It flows southeast, then west, through Mendocino National Forest and Lake County. It is impounded in Lake Pillsbury, the reservoir created by Scott Dam.
Below Lake Pillsbury the Eel River re-enters Mendocino County, turning northwest approximately 15 miles east of Willits. It flows northwest in a long isolated valley, collecting many tributaries including the Middle Fork Eel River and the North Fork Eel River. Between these two tributaries the Round Valley Indian Reservation lies east of the Eel River.
After the North Fork confluence, the Eel River flows around Island Mountain in the southwestern corner of Trinity County then crosses Humboldt County from the southeast to northwest, flowing in a winding course past a series of small mountain communities. The South Fork Eel River joins as the river valley widens. U.S. Route 101 runs along the South Fork Eel River and then the main Eel River's lower course.
After passing Scotia Bluffs near Rio Dell, the Eel River is joined by the Van Duzen River. Below that confluence, the Eel passes Fortuna and enters the Pacific in central Humboldt County, approximately 15 miles south of Eureka. Eel River estuary is recognized for protection by the California Bays and Estuaries Policy.
The Northwestern Pacific Railroad follows the Eel River from Dos Rios to Fortuna.