The South Fork Snake River (SFSR) currently supports one of the few remaining functioning populations of fluvial Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri (YCT) within their native range, and is the strongest population in Idaho. Since 2004, the Idaho Department of Fish and Game (IDFG) and collaborators have implemented an intensive YCT conservation management strategy in the SFSR drainage. This BPA contract assists IDFG management efforts on the SFSR. The SFSR, associated habitat, and fauna comprise an ecologically and economically significant resource. The quality fish and wildlife habitat is largely attributed to the cottonwood riparian gallery along the river corridor. The cottonwood riparian gallery and YCT population evolved with the dynamic flows of the SFSR, a snow-melt driven system with naturally high spring flows. The construction of Palisades Dam has altered river flows. Further impacts to the YCT population have resulted from the establishment of a self-sustaining, non-native, Rainbow Trout O. mykiss (RBT) population.

One of the management strategies is intensive weir management to protect tributaries from RBT invasion and the genetic integrity of the native YCT tributary spawning migrations. IDFG operates and maintains the modified fish weirs and traps on four tributaries through the spring spawning migrations. Pine, Rainey, and Palisades creeks have electrical barriers and Burns Creek incorporates both a waterfall and a velocity barrier. Yellowstone Cutthroat Trout are placed upstream of the barrier and RBT and Rainbow Trout × Cutthroat Trout hybrids are removed. Research has indicated that maintenance and operation of the weirs is a critical component in the suite of management strategies designed to conserve and ensure population viability of YCT in the SFSR. The IDFG is committed to protecting the genetic integrity of YCT in the four major spawning tributaries of the SFSR over the long-term, recognizing that this effort must continue annually and will induce periodic maintenance and repair costs.

Along with RBT removals, YCT are tagged with passive integrated transponders (PIT) in the SFSR drainage since 2008 and these tag data are providing substantial insights into YCT 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. We anticipate concluding investigations using PIT tags in 2030.

The remainder of the work associated with this contract focuses on improving YCT abundance, particularly in Rainey Creek, adult spawner abundance is severely depressed. Rainey Creek is the largest drainage of the four major spawning tributaries, but supports less than 1% of the cumulative YCT spawners in these tributaries. The spawning migration of fluvial YCT in Rainey Creek have been impacted by entrainment of fish by irrigation diversions, loss of quality habitat through grazing and agricultural practices along the lower reaches of Rainey Creek, and connectivity issues with low instream flows during dry years. Efforts to increase adult returns in Rainey Creek include stocking eyed-eggs of wild-origin, and improving degraded habitat through stream habitat restoration.