The South Fork Snake River in eastern Idaho from Palisades Dam near the Idaho/Wyoming border downstream to its confluence with the Henrys Fork currently supports one of the few remaining functioning populations of fluvial Yellowstone cutthroat trout within their native range, and is the strongest population in Idaho. However, this population is threatened by non-native rainbow trout. Since 2004, the Idaho Department of Fish and Game (IDFG) and collaborators have implemented an intensive Yellowstone cutthroat trout conservation management strategy in the South Fork Snake River drainage composed of three parts. This three-pronged management approach includes managing water releases from Palisades Reservoir during spring to benefit cutthroat trout spawning while hampering rainbow trout recruitment, protecting the genetic integrity of critical cutthroat trout spawning tributaries from hybridization risks with rainbow trout, and reducing competition and hybridization risks by increasing angler harvest of rainbow trout and rainbow x cutthroat trout hybrids. Recent weir modifications have greatly improved IDFG’s ability to protect the tributaries from rainbow trout invasion. IDFG is committed to protecting the genetic integrity of cutthroat trout in the four major spawning tributaries of the South Fork Snake River over the long-term, recognizing that this effort must continue annually and will induce periodic maintenance and repair costs.

The four major spawning tributaries to the South Fork are Burns, Pine, Rainey, and Palisades creeks. IDFG will operate and maintain the modified fish weirs and traps on all four tributaries through the spring spawning runs from mid-March through July annually. Each of the tributaries have a barrier to fish migration adjacent to an upstream fish trap. Pine, Rainey, and Palisades creeks have electrical barriers and Burns Creek incorporates both a waterfall and a velocity barrier. Migrating trout will be forced into the fish trap where IDFG will hand sort individual fish on a daily basis. Cutthroat trout will be placed upstream of the barrier and rainbow trout and rainbow x hybrid trout will be removed and transported to a nearby kids fishing pond. Cutthroat trout passed upstream will be marked with PIT tags or fin punches. Near the end of the spawning run, IDFG will capture fluvial-sized trout upstream of the fish weirs and inspect each fish for marks. The percentage of marked fish will be used as a measure of trapping efficiency. With the newly modified weirs, trapping efficiencies have been high, and we anticipate high efficiencies to continue. In order to maintain high trapping efficiencies, periodic maintenance such as slight channel modifications, removal of sediment, and replacement or repair of damaged equipment or software will be required to keep the weirs  functional.


With invasion of fluvial rainbow trout precluded in the spawning tributaries, IDFG will reduce the abundance of resident rainbow trout that have  established populations in 9.6 km (6 miles) of Palisades Creek upstream of the fish weir and an unknown number of kmupstream of the Burns Creek fish weir. Backpack electrofishing units will be used to remove rainbow trout and rainbow x cutthroat trout hybrids through the entire reach known to support resident rainbow trout on an annual basis for five years. Effectiveness of the removal efforts will be evaluated using the species composition of total catch.

The second part of this contract pertains to entrainment of Yellowstone cutthroat trout into irrigation canals which is not addressed by IDFG’s three-pronged management plan. Water from the South Fork Snake River is used to irrigate more than 670,000 acres in eastern and southern Idaho. IDFG and partners have screened diversions off the four major spawning tributaries of the South Fork, but several large diversions off the main river are not screened. The largest of these diversions is the Great Feeder, the diversion for the Dry Bed Canal, which is a large canal allocated up to 142 cubic meters per second (5,000 cfs) during the peak growing season. This is often half of the South Fork Snake River’s total volume. General movement information from
PIT-tagged cutthroat trout and creel surveys conducted in the canal, indicate the Great Feeder and other large diversions are sinks for the cutthroat trout population, but the impact has not been quantified. An improvement project, such as screening these large canals would be expensive and will first require a thorough understanding of the magnitude of entrainment impacts on the cutthroat trout population and a list of best alternatives for possible solutions. We propose to quantify entrainment of Yellowstone cutthroat trout and other trout species into the large canal that are diverted through the middle portion of the South Fork Snake River. Once entrainment is quantified, we propose to create a prioritized alternative list to mitigate for or eliminate
entrainment and start the implementation of the best alternative(s).