Rainbow trout, of generally small size, are the predominant fish throughout the drainages, except for some headwaters and a few minor tributaries where brook trout are dominant. Native bull trout and cutthroat are maintaining fishable populations in some limited areas. Mountain whitefish are found only in the Big Lost drainage.
Stream quality and fish populations vary from excellent to poor where streams alternately intersect and perch above the groundwater table or enter irrigation ditches. Streams become marginal where they flow into the Snake River Plain due to diversion and freeze out. Where groundwater inflow is lacking, wintertime air temperatures often cause streams to become icebound and leave their channels. Severe habitat degradation has occurred to most streams due to past and/or present grazing practices on private and public range land. Natural flood events have also severely impacted some drainages, such as Wildhorse Creek in the Big Lost River Drainage.