The Blackfoot River Watershed is a world renown native trout fishery, supporting increasing numbers of fluvial bull trout and westslope cutthroat.

The valley is part of the Northern Continental Divide Ecosystem which supports the largest population of grizzly bears in the lower 48 states.  Grizzly bears, gray wolf, wolverine, and lynx are year-round residents.

The native grassland/scrub communities provide habitat for Columbian sharp-tailed grouse, one of only two remaining populations in Montana.  The prairie pothole and riparian habitats are home to over 200 species of migratory birds including black terns, greater sandhill cranes, and long-billed curlews.

Over 600 species of vascular plants occur in the watershed with nearly 30% found in the glaciated wetlands.  Six rare or uncommon plant communities occur in the Blackfoot Valley, including the three-tip sagebrush/tough fescue plant association found nowhere else in the world.