The forest consists of high desert grasslands, sage, juniper, pine, fir, and other tree species.

The forest was established by President Theodore Roosevelt on June 13, 1908, and is named after the Malheur River, from the French, meaning "misfortune".

It is managed by the United States Forest Service for timber extraction, cattle grazing, gold mining and wilderness use.

[5] In descending order of land area, the forest is located in parts of Grant, Harney, Baker, and Malheur counties.

[6] There are three ranger districts in the forest, with offices in John Day, Prairie City, and Hines.