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The Malheur River is a tributary of the Snake River, approximately 165 miles (266 km) long, in eastern Oregon in the United States. It drains a high desert area, between the Harney Basin and the Snake. Despite the similarity of name, the river does not flow into nearby Malheur Lake, which is located in the enclosed Harney Basin southwest of the watershed of the river.
The river rises in the southern Blue Mountains of southern Grant County, south of Strawberry Mountain in the Strawberry Mountain Wilderness. It flows south through Malheur National Forest, then southeast past Drewsey and through Warm Springs Reservoir. At Riverside in eastern Malheur County it receives the South Fork Malheur River from the south, then turns sharply back northward to Juntura, where it receives the North Fork Malheur River form the north. From Juntura it flows generally east past Vale, joining the Snake from the west approximately 2 mi (3 km) north of Ontario, Oregon. The mouth of the Malheur River is approximately at Snake river mile 370.