Snowshoe Peak in the Cabinet Mountains Wilderness, at 8,738 feet (2,663 m), is the highest peak within the forest. Mountain ranges included in the forest include the Whitefish, Purcell, Bitterroot, Salish, and Cabinet ranges.
The Kootenai and the Clark Fork rivers are the major rivers and are fed by abundant rainfall that is more than double that amount found elsewhere in Montana. Three major hydroelectricdams exist in the Kootenai National Forest. Libby Dam on the Kootenai River creates a 90-mile (140 km)-long lake known as Lake Koocanusa (a play on Kootenai-Canada-United States of America), which extends into Canada. The shores of the lake are all forested with no private property easements. The lowest elevation in Montana is where the Kootenai River leaves the state, 1,832 feet (558 m) above sea level. Other rivers in the forest include the Yaak, Fisher, Tobacco and Vermillion, with water flowing from over 100 lakes.
The climate of the Kootenai has been described as "modified Pacific maritime" in character, meaning that compared to the remainder of Montana, this area's climate resembles that found along the Pacific coast. The character becomes "modified" by occasional intrusions of arctic air masses, more common elsewhere in Montana, which can bring winter temperatures down to −30 °F (−34 °C). Winters also feature heavy snowfalls in the mountains.
The national forest is located overwhelmingly (almost 95 percent) in Lincoln County, Montana, but extends into neighboring counties. In descending order of forestland area, they are Flathead County in Montana, Bonner and Boundary counties in Idaho, and Sanders County in Montana.