The habitat diversity of the Refuge supports a wide variety of wildlife species. At least 14 species of migratory and breeding waterfowl utilize wetland areas. These include mallard, gadwall, cinnamon teal, green-winged teal, lesser scaup, wood duck, redhead, common goldeneye and Canada geese. Various species of marsh and shorebirds are present during the summer months. These include grebes, herons, gulls, killdeer, sandhill cranes, dowitchers, sandpipers, common snipe, bitterns and black terns.
Upland game bird species include spruce grouse, blue grouse and ruffed grouse. The Refuge lies within the historic range of the Columbian sharp-tailed grouse.
Raptor species such as northern harriers, red-tailed hawks, Swainson's hawks, American kestrels and great-horned owls are present.
Resident mammal species include white-tailed deer, mule deer, elk, moose and black bear. Furbearers include fisher, pine martin, lynx, wolverine and bobcat. Muskrat, badger and Columbian ground squirrels are also present on the Refuge.
The threatened grizzly bear and the endangered gray wolf are known to inhabit the Pleasant Valley Area.
Prior to acquisition, Refuge lands were privately owned and managed as the cattle and horse ranch known as Lost Trail Ranch. The ranch's long and diverse history of cattle ranching dates back to the late 1800's. Lost Trail National Wildlife Refuge was acquired in August of 1999. It is the 519th Refuge in the National Wildlife Refuge System. This national system comprises over 93 million acres of wildlife lands across the country.
Because the Refuge is newly established, many public use activities are not allowed at this time. Refuge policy and regulations require the development of various public use plans before public use can be allowed. These plans will receive public input during the administrative planning process.
Public use activities that are currently allowed under an interim compatibility determination are: wildlife observation, environmental interpretation and wildlife photography. There are no viable fish populations on the Refuge which would allow for public fishing activity. The Refuge is currently not open to hunting.