Most trout downstream from Blackfoot Reservoir have escaped from the reservoir or are hatchery rainbow planted directly into the river. Mountain whitefish are the dominant game fish species in river sections downstream from Wolverine Creek.
Trout population in Blackfoot Reservoir varies from 46% to 80% hatchery rainbow, with the balance being composed of hatchery Bear Lake and Wild Yellowstone cutthroat. Wild cutthroat make up about 90% of the population in the river and tributaries upstream from Slug Creek.The Blackfoot River, its tributaries, and the Blackfoot Reservoir serve integral roles in the life history and ecology of wild cutthroat trout. Mature cutthroat from the reservoir ascend the river in April and May and enter upper tributaries to spawn in late May and June. Progeny rear in the tributaries for varying periods up to two years. Most juvenile cutthroat trout return to Blackfoot Reservoir after rearing one, two, or three years in the streams. They stay in the reservoir until ready to start the spawning cycle.