The Ventura River Watershed drains approximately 228 square miles. The Matilija Creek Basin is part of the Ventura River Watershed and drains approximately 55 square miles. The creek runs about 15 miles from its headwaters in the Santa Ynez Mountains in Santa Barbara County, through the Matilija Wilderness in Ventura County to where it is impounded by the Matilija Dam.
Below the dam, at the confluence of Matilija Creek and the North Fork of Matilija Creek, the river becomes the Ventura River.
The Ventura River then continues another 15 miles to where it enters the Pacific Ocean near Ventura. The river once hosted Southern California steelhead. The Matilija Dam (and other barriers on tributaries to the Ventura) block fish passage in the watershed.