Many remain open through the fall hunting season. The Kootenai is heavily forested. As a multiple use Forest there has been an extensive system of logging roads built in the past 75 years and many areas on the Forest are in various stages of regeneration. Trees native to the area include western red cedar, western hemlock, western white pine, lodgepole pine, ponderosa pine, alpine larch, western larch, mountain hemlock, grand fir, subalpine fir, whitebark pine, Douglas-fir, Engelmann spruce and juniper. Cottonwood, quaking aspen, alder, and paperbirch grow in the moist sites and valley bottoms.
Vegetation is dense at lower elevations and along the streamsides.
Hundreds of plant species have been identified in the Forest. Common understory shrub species include huckleberry, snowberry, ninebark, mountain maple, menziesia, spirea, service berry, bitterbush, chokecherry, wild rose, ocean spray, syringa, kinnikinnick and dogwood. With the wide range of elevations, plant species range from cactus in the Tobacco Valley to fairy slipper orchids hiding in deep forest shade. Some of the wildflowers found on the Forest are violets, lupine, trillium, sego lily, spotted coralroot, buttercups, columbine, queencup beadlily, arrowleaf balsamroot, beargrass, clematis, pinedrops, phlox, harebell and Indian paintbrush. Bitterroot, the Montana State flower , can also be found on some of the mountain slopes.