The Malheur 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 western 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 from the north. From Juntura it flows generally east past Vale, joining the Snake from the west approximately north of Ontario, Oregon. The mouth of the Malheur River is approximately at Snake river mile (RM) 370 or river kilometer (RK) 600.