Thomas Fork Fish Passage and Habitat Restoration

The Thomas Fork is a fourth order tributary to the Bear River that drains a 150,100 acre watershed in southeastern Idaho and western Wyoming. Bonneville cutthroat trout occur throughout the drainage, and tributaries support some of the most genetically pure populations of the subspecies within its native range. The Thomas Fork, the neighboring Smiths Fork, and sections of the Bear River between the two, provide a tenuous link between these tributary populations and constitute what is likely the last connected large river habitat available to BCT.  Large fish in this system are migratory, using habitats in the lower elevation, mainstem rivers for growth and maintenance and moving large distances (up to 90 km) to headwater habitats to spawn. Unfortunately, diversion structures along the lower Thomas Fork blocked BCT spawning migrations and trapped downstream migrants in irrigation canals, and historic land-use practices degraded riparian habitats, accelerated stream bank erosion, increased water temperatures, and reduced the availability of clean spawning gravels and deep water habitats that BCT require. 

Reestablishing watershed connectivity has become a major focus of stream restoration efforts and is especially important to migratory populations in which individuals require different habitats at different life stages. Adult feeding and overwintering habitats in the Bear River are many miles from spawning and juvenile rearing habitats in Thomas Fork and Smiths Fork tributaries. During low water years Thomas Fork diversion structures prevent adult spawners from moving between mainstem reaches of the Thomas Fork and Bear River and spawning habitats upstream in the Thomas Fork. During high run-off years adult spawners are able to bypass irrigation structures and move upstream before irrigation activities begin. However, in those years up to 30% of post-spawn adults are ultimately trapped and killed in irrigation canals as they attempt to return to mainstem habitats.

In addition to the fragmentation of BCT habitats caused directly by movement barriers, the Thomas Fork also presents significant indirect challenges to watershed connectivity due to poor water quality and degraded habitat for BCT and other aquatic organisms. During spring run-off, stream flows in the watershed can range from 100 to 1000 cubic feet per second (cfs) and transport a large pulse of bacteria, nutrients and dissolved solids introduced from dairy farms, cattle feeding operations, and stream bank erosion.  Water quality monitoring indicates that up to 30% of the nitrogen, phosphorous, and suspended sediment found downstream in the Bear River originates in the Thomas Fork. As a result of this sediment and nutrient loading, both the lower Thomas Fork and Bear River have been designated as ‘water quality limited’ by the Idaho Department of Environmental Quality. Sediment inputs reduce the availability of clean spawning gravels and contribute to elevated water temperatures. Nutrient pulses increase plant and algal biomass and reduce the amount of oxygen available to aquatic organisms. The combined effect of these inputs is to render many reaches of the lower Thomas Fork seasonally uninhabitable, and sometimes completely impassable, to BCT.

Trout Unlimited’s restoration efforts in the Thomas Fork have focused on a two-pronged approach of first restoring critical migration corridors between habitats and then improving instream habitat and water quality by stabilizing streambanks and reestablishing riparian communities.

Peterson Diversion
The Peterson Diversion is the lowest migration barrier on the Thomas Fork, located roughly one mile upstream from the confluence with the Bear River. This diversion has been documented as blocking 100% of upstream fish migrations during dry years when the diversion boards often remain in place year round. In 2006, Trout Unlimited, in partnership with the landowner, the U.S. Fish and Wildlife Service, Idaho Department of Fish and Game, and the Bear Lake Regional Commission constructed a semi-natural channel bypass around the diversion to accommodate upstream migrations, and installed a rotary drum fish screen in the irrigation canal to prevent entrainment of fish during irrigation season.

Mumford Diversion
The Mumford Diversion is the middle irrigation diversion on the Thomas Fork, located between the Peterson and Taylor diversions. The Mumford Diversion is the senior water right on the Thomas Fork, and, at times, diverts almost 100% of the streamflow in the Thomas Fork into the irrigation canal. In 2004 Trout Unlimited teamed up with the U.S. Forest Service, U.S. Fish and Wildlife Service, Idaho Department of Fish and Game, Faucet Irrigation Company, and the landowner to install a fish screen and fish ladder bypass at the Mumford Diversion to prevent entrainment and allow fish passage around the diversion dam. 

Taylor Diversion
The Taylor Diversion is the most upstream full-spanning diversion on the Thomas Fork, and, as such, is the first significant obstacle that migratory BCT encounter during their return trip from tributary spawning habitat to mainstem overwintering habitat. A study conducted by researchers from the University of Wyoming documented that 9 of 15 radio tagged BCT that attempted to move downstream past this diversion during the summer were trapped and killed in the irrigation canal. In 2004, Trout Unlimited and the U.S. Forest Service, along with the same group of project partners that was working on the Mumford Diversion project, installed a fish screen and bypass ladder at the Taylor Diversion to prevent entrainment and allow for upstream and downstream migrations past the diversion structure.

Thomas Fork Habitat Restoration
To restore riparian and instream habitat and improve water quality project partners used heavy equipment to mechanically return the eroded, vertical stream banks to a 3:1 slope, as suggested by the Natural Resources Conservation Service (NRCS) as suitable for revegetation of riparian species. Reducing the bank angle also provided more floodplain to dissipate energy during high streamflow events and reduced the risk of flooding downstream. Rock from local quarries was placed over the exposed soil and along the toe of the slope at the water’s edge to protect against erosion until grasses and other vegetation take root and begin to stabilize the stream bank. We also used flow deflectors to absorb energy and redirect streamflow away from especially vulnerable areas. These flow deflectors will also hasten the reduction of the channel width to depth ratio and create areas of lower water velocity to develop gravel bars. We then planted the newly restored stream banks with native vegetation. 

We expect that BCT habitat will improve quickly following bank stabilization and revegetation. By reducing bank angles, initially armoring erosion prone areas with rock, and reestablishing riparian communities through a combination of seeding and transplanting willow cuttings and mature clusters, we significantly reduced sediment and nutrient inputs into the Thomas Fork almost immediately. As riparian communities establish themselves, root systems will stabilize stream banks and absorb nutrients, and foliage will provide overhead cover and shade for the stream. The combination of bank stabilization, flow deflectors, and revegetation will ultimately reduce the channel width to depth ratio, increase cover for fish and other aquatic organisms, moderate water temperatures, and improve water quality in the Thomas Fork and the Bear River.

Photos of Mast streambank restoration project before (top photo) and after (bottom photo) streambank stabilization treatments.