Malheur Lake is one of the lakes in the Malheur National Wildlife Refuge in Harney County in the U.S. state of Oregon. Located about 18 miles (29 km) southeast of Burns, the lake is marsh fed by the Donner und Blitzen River from the south and the Silvies River from the north. Malheur Lake periodically overflows into Mud Lake to the west and thence to Harney Lake, the sink of Harney Basin.

The western area of Malheur Lake consists of ponds separated by small islands and peninsulas. The lake's central and eastern sections are more open. The generally shallow water is suitable habitat for migratory birds, waterfowl, and aquatic plants.

As is typical of Great Basin lakes, Malheur Lake's surface area changes dramatically with the local weather, climate, and season because the lake is in a very flat basin. A large influence on the water volume is local snow melt, especially from Steens Mountain, south of the lake. For example, large snowpacks in the mid-1980s caused the lake to expand from approximately 67 to 160 square miles (170 to 410 km²) within three years, flooding usually dry areas and damaging a branch of the Oregon Eastern Railway. Soon afterward, drought in the early 1990s reduced the lake size to just 200 acres (0.31 sq mi), exposing large mudflats and dusty playas.