The Northwest portion of the Basin lies in mountainous terrain. Wooded areas consist primarily of mixed fir and pine forest in the higher elevations with ponderosa pine and western Juniper in the transition zones. Sagebrush and grass communities dominate the uplands. Low-elevation terraces and flood plains are occupied primarily by irrigated cropland in the lower basin valleys. Stream gradient in the Malheur River is characteristic of southeastern Oregon streams as described by Bowers et al.
Steep gradient limits fish movement.
The mainstem through the forest down stream to Namorf Dam has stream gradient and riffle frequency characteristic of trout habitat. Gravel bar deposits, islands and new channels are formed by constantly shifting bedload. Fine bedload material settles out forming compact banks and a deep meandering single channel. The lower velocity combined with poor water quality limit game fish production. In, general, the streams of the Malheur subbasin possess characteristics attributable to the semi-arid climate.