The Harney Basin is an endorheic basin in southeastern Oregon in the United States at the northwestern corner of the Great Basin. One of the least populated areas of the contiguous United States, it is located largely in northern Harney County, bounded on the north and east by the Columbia Plateau—within which it is contained, physiographically speaking—and on the south and west by a volcanic plain. The basin encompasses an area of 1,490 square miles (3,859 km2) in the watershed of Malheur Lake and Harney Lake. Malheur Lake is a freshwater lake, while Harney Lake is saline-alkaline.

The Malheur River is a 190-mile-long (306 km) tributary of the Snake River in eastern Oregon in the United States. It drains a high desert area, between the Harney Basin and the Blue Mountains and the Snake.