Coyote Creek will be managed for self-sustaining native fish populations including speckled dace, desert sucker, Sonora sucker, roundtail chub, and loach minnow. The lower portion is considered critical habitat for loach minnow. Much of Coyote Creek has minimal flow or is dry entirely. Future management considerations include re-establishing loach minnow populations in the lowest portion near the confluence of the East Fork Black River, where water levels may stay more consistent.