The South Fork Snake River has been called Idaho's most unique riparian ecosystem containing the largest continuous cottonwood ecosystem in the state. The South Fork provides habitat for nine nesting bald eagle pairs and up to 100 wintering eagles. The U.S. Fish and Wildlife Service considers this river section to be the most important fish and wildlife habitat in the state of Idaho.
In the South Fork Snake River and tributaries below Palisades Dam, wild native cutthroat trout are a mixture of both fine-spotted and Yellowstone races. Fine-spotted cutthroat are stocked as sub-catchables and catchables into Palisades Reservoir and some are flushed into the South Fork with reservoir drawdowns.
Although exotic wild rainbow, hybrid, and brown trout provide a significant component of the catch throughout the South Fork drainage, they pose a potential threat to the genetic integrity and long-term viability of wild cutthroat populations. Stocking in the mainstem and tributaries was discontinued in the early 1980s.
Mountain whitefish are the most abundant game fish in the drainage.
Habitat in the South Fork mainstem is generally in good condition. Winter flow releases, regulated to manage Palisades Reservoir storage, have resulted in significant dewatering of secondary channels of the South Fork. The dewatering causes major losses of juvenile salmonids during winter.