It drains part of the eastern side of the Sierra Nevada in the watershed of Walker Lake in the Great Basin.

The East Walker River rises from snow melt in the Sierra Nevada of eastern California north of Mono Lake and near the northeast boundary of Yosemite National Park.

[3] Below Bridgeport Reservoir, the East Walker River flows northeast through the Sweetwater Mountains, where it crosses the state line into southern Lyon County, Nevada and skirts to the south of the Pine Grove Hills before flowing north to join the West Walker River approximately 7 mi (13 km) south of Yerington to form the Walker River.

By-Day Creek, a tributary to Buckeye Creek, is believed to contain the last pure native Lahontan cutthroat trout (LCT) Oncorhynchus clarkii henshawi population in the Walker River basin and was never stocked with other species of fish.

[citation needed] Ranchers have placed barbed wire across the river on both the California and Nevada sides.