Ninepipe National Wildlife Refuge sits in the Rocky Mountain Trench near the base of the Mission Mountains within the Flathead Indian Reservation. The valley was shaped by glacial activity during the Pleistocene, and the terrain is rolling grasslands interspersed with pothole wetlands that contain water year-round during wet years.
The IBA consists of the national wildlife refuge, which is owned by the Confederated Salish and Kootenai tribes, and a state wildlife management area that surrounds the refuge. The main feature of the refuge is Ninepipe Reservoir, which is managed by the Bureau of Indian Affairs for irrigation and flood control in addition to serving as a wildlife refuge.
Ninepipe Reservoir has breeding colonies of Western Grebes, Red-necked Grebes, Double-crested Cormorants, Great Blue Herons, California Gulls, Ring-billed Gulls, and Yellow-headed Blackbirds, although recent count data are lacking for these species. At least 11 species of ducks nest here in good numbers, as do small numbers of American Bitterns and Caspian Terns. Thousands of waterfowl, mostly Canada Geese and Mallards, congregate in ice-free portions of the reservoir during some winters, and Bald Eagles also are relatively common at this time of year.
The refuge is used by fishermen and birdwatchers, but no boats are allowed, and most of the refuge is closed during spring and summer to minimize disturbance to nesting birds. Nonetheless, the number of people in the Mission Valley is growing rapidly, and human disturbance to waterbirds remains a potential problem. The national wildlife refuge proper (which includes the reservoir) is closed to hunting, although adjoining state wildlife management area lands are open to public hunting of waterfowl and introduced galliforms.
Ninepipe National Wildlife Refuge is under long-term lease to the U.S. Fish and Wildlife Service from the Confederated Salish and Kootenai Tribes. The IBA includes Ninepipe NWR proper (835 ha) plus the adjacent Ninepipe Wildlife Management Area (1570 ha), owned by Montana Fish, Wildlife, and Parks.
The IBA is centered around Ninepipe Reservoir, which contains several small islands and is ringed by emergent vegetation. Managed grasslands surround the reservoir, with the dominant grasses made up of exotic species.
The refuge is superimposed on a reservoir that contains about 675 ha of water when full. The Bureau of Indian Affairs Flathead Irrigation Project manages the reservoir for irrigation and flood control. Fishing is allowed from shore on Ninepipe Reservoir in accordance with state and tribal regulations. Photography and wildlife observation are encouraged. A Watchable Wildlife viewing area off Highway 93 was established jointly by the USFWS, the Montana Department of Fish, Wildlife and Parks, and the Confederated Salish and Kootenai Tribes. There is a short, accessible trail along the shore of the reservoir with interpretive signs about wildlife and habitat. Portions of the refuge are closed during the spring to minimize human disturbance to nesting birds. The Refuge is closed to hunting. Adjoining state-owned Wildlife Management Area lands are managed for wildlife cover, food production, and public hunting. The closure of Ninepipe NWR enhances the quality of hunting in the Flathead Valley by providing a sanctuary which may keep more birds in the area for a longer period of time.
The 1948 Act stated that the Confederated Salish and Kootenai Tribes "shall have the right to use such Tribal lands, and to grant leases or concessions thereon, for any and all uses not inconsistent with such permanent easement." Cattle grazing is conducted with a deferred rotational system worked out with the Tribes and allowed with a Memorandum of Understanding with the U.S. Fish and Wildlife Service.