Ninepipe is a prime nesting habitat for numerous bird species such as the grebe, Canada goose, bittern, great blue heron and various species of ducks. Nesting platforms for ospreys at one end of the lake provide added habitat for this predatory species. Mammals include muskrat, badger and porcupine live within the refuge, and grizzly bears have been known to venture out of the Mission Range mountains onto the refuge.
