Boggy Creek was formerly occupied by hybridized Apache trout, though lower flows have made available habitat marginal and unable to support a trout population. Should flows be restored, Boggy Creek will be managed as an Apache trout stream, and is protected by a downstream fish barrier on Centerfire Creek. Boggy Creek will secondarily be managed for populations of speckled dace and bluehead sucker. Riparian habitat management will also take into account the New Mexico meadow jumping mouse, currently understood to be present
