Lost River begins and ends in a closed basin in northern California and southwestern Oregon in the United States. The river, 60 miles (97 km) long, flows in an arc from Clear Lake Reservoir in Modoc County, California, through Klamath County, Oregon to Tule Lake in Siskiyou County. About 46 miles (74 km) of Lost River are in Oregon, and 14 miles (23 km) are in California.
From its source, the river flows into Langell Valley, where Miller Creek enters from the right. Near Bonanza, the river turns west and passes through Olene Gap, about 10 miles (16 km) east of Klamath Falls.Dams, canals, pumps, and other artificial structures on Lost River, Clear Lake, and Tule Lake are part of the Klamath Project of the U.S. Bureau of Reclamation, which manages the basin's water flow mainly for farming and flood-control.