Cottonwood Creek is a southeastward-flowing 4 mi (6.4 km) tributary stream of San Luis Creek, originating in the eastern foothills of the Diablo Range in Merced County, California. The creek's mouth, before the San Luis Dam was built across the course of San Luis Creek, was originally at its confluence with San Luis Creek at approximately 250 ft (76 m). Today, Cottonwood Creek enters San Luis Reservoir, which raises the elevation of the creek's mouth to 548 ft (167 m), where it becomes Cottonwood Bay on the north side of the reservoir. The source of the creek is at Red Hill, a summit on the eastern slope of the Diablo Range.