The San Benito River drains a 530 square miles (1,400 km2) watershed and flows roughly along the San Andreas Fault between the Gabilan Range to the west and the Diablo Range and south Santa Clara Valley to the east.

From its headwaters at elevation at 4,760 feet (1,450 m) beginning southeast of Santa Rita Peak in the Diablo Range at extreme southern San Benito County, the river flows to Hernandez Reservoir, formed by a dam built in the early 1960s for irrigation supply and flood control.

In portions of the river you will find homeless camps, trash, concrete, evidence of mining damage, and the occasional fossil.

After restoration of trash removal near the mouth of the San Benito River by the conservation group, CHEER, juvenile steelhead trout (Oncorhynchus mykiss) returned, indicating that successful spawning and rearing habitat is now present after a 75 year absence.

[5] In a 1940 correspondence, California Department of Fish and Wildlife (CDFW) stated that San Benito Creek "is a good trout stream in its headwaters" with "considerable runs of sea-run steelhead" in some years.