Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri (YCT) are the native trout of the South Fork Snake River (SFSR). The river supports the strongest remaining fluvial population within their historical range in Idaho and is one of only a handful of rivers in the species’ native range which supports robust populations of YCT. Across the majority of the species range, YCT have experienced dramatic reductions in abundance and distribution. In August 1998, conservation groups petitioned the United States Fish and Wildlife Service (USFWS) to list Yellowstone cutthroat trout under the Endangered Species Act (ESA). In February 2001, the listing petition was denied, and conservation groups filed a lawsuit in January 2004 which led to a 12-month review of the current status of YCT. The USFWS determined that YCT did not warrant listing under the ESA in February 2006. However, ESA listing petitions may occur again as YCT have continued to sustain declines in their abundance and distribution across their historical range. The work funded under this project represents a significant portion of the work that IDFG conducts to help sustain the South Fork Snake River population of Yellowstone Cutthroat Trout.

The South Fork Snake River (SFSR), comprising about 60 river miles from Palisades Dam downstream to the Henrys Fork Snake River confluence, not only supports an ecologically important YCT population, but also an economically important recreational fishery for YCT, Brown Trout (Salmo trutta), and Rainbow Trout (O. mykiss) and Rainbow Trout × Cutthroat Trout hybrids (collectively referred to as RBT). The primary management objective Idaho Department of Fish and Game (IDFG) has for the SFSR is the preservation of the genetic integrity and population viability of YCT. Another objective is the reduction in the numbers of RBT to no more than 10% of the total trout population. These objectives are being pursued through multiple approaches that align with our State Fish Management Plan and YCT Management Plan. The first approach is to prevent upstream migration of RBT into the four major SFSR spawning tributaries via trapping at weirs (the work funded under this project). The second approach is to reduce RBT abundance through increased angler harvest. Estimable numbers of RBT were first sampled in 1989, and the three-pronged approach was first implemented in 2004, following initial research that identified spatiotemporal overlap in spawning between RBT and YCT coupled with population trend data indicating YCT were being replaced by a growing RBT population. This research also indicated fish abundance trends were likely driven by hydrologic alteration due to Palisades and Jackson Lake dams which had potential negative effects on YCT and positive effects on RBT.

This BPA contract assists IDFG management efforts on the SFSR by supporting elements of one of the three management prongs: tributary weirs and the health of YCT tributary runs. The four major spawning tributaries where native fluvial YCT spawn in the SFSR system are Burns, Pine, Rainey, and Palisades creeks. IDFG operates and maintains the modified fish weirs and traps on all four tributaries through the spring spawning runs from April through mid-July, annually. Each of the tributaries has 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 are forced into fish traps where IDFG hand sorts individual fish daily. Cutthroat Trout are placed upstream of the barrier and RBT are removed and transported to nearby kids' fishing ponds. Cutthroat Trout passed upstream are marked with PIT tags or fin punches. Near the end of the spawning runs, IDFG captures fluvial-sized trout upstream of the fish weirs and inspects each fish for marks. The percentage of marked fish is 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 is required to keep weirs functional. Research has indicated that operation of the weirs, and the spawning refugia for YCT from RBT created by the weirs, is a key component to the long-term population viability of YCT in the SFSR. Because the SFSR supports the most robust population of fluvial YCT in the state, the management efforts funded in this contract are a high priority for IDFG among work funded by BPA, and IDFG is committing to operating the weirs and monitoring YCT population trends into the foreseeable future. PIT-tagging efforts have occurred in the SFSR drainage since 2008 and are providing substantial insights into movement, spawning behavior patterns, survival rates, and effects of interactions with RBT. The results of this work are being used to focus current and future management efforts.

The remainder of the work associated with this contract focuses on improving the health of spawning runs, particularly in Rainey Creek, where runs are severely depressed. Rainey Creek is the largest drainage of the four major spawning tributaries, but receives roughly 30 returning YCT spawners compared to 3,000 spawning YCT in the adjacent drainage, Pine Creek. Runs of YCT in the Rainey Creek have been impacted by entrainment of fish in irrigation diversions, loss of quality habitat through grazing and agricultural practices along the lower reaches of Rainey Creek, and connectivity issues with low discharges remaining in-channel during dry years. Factors affecting YCT runs in Rainey Creek which can be affected by IDFG include fish abundance and habitat quality. The goal is to increase the abundance of spawning adult YCT returning to Rainey Creek. Efforts to increase YCT returns in Rainey Creek include stocking eyed-eggs of wild-origin, and improving degraded habitat through habitat restoration.