Science and Technology

The HFF science and technology program contributes to efforts aimed at promoting favorable streamflow, good water quality, healthy fish populations, and a positive fishing experience. More than 100 research and monitoring projects to date have provided a scientific basis for management and decision-making in the Henry's Fork watershed. HFF works cooperatively with federal and state agencies, academia, and nonprofit organizations to develop, fund, and complete projects.


Fish Habitat

A great deal of research was conducted on fish habitat, especially in the Railroad Ranch reach, to answer the question “What limits the trout population and how can we increase it?”. Much of this research was conducted between the mid-1980s and late 1990s by graduate students of Dr. Jack Griffith of Idaho State University, with additional research conducted in 2013-2014 by graduate student Zach Kuzniar. What follows is a very simplified summary of five key findings related to Ranch habitat. To learn more about each topic or research effort, follow the links provided or visit us at the HFF Community Campus for additional resources.

1.  By the mid-1990s, research identified winter survival of juvenile rainbow trout as the most significant factor limiting the population in the reach from Island Park Dam to Hatchery Ford. (Gregory, 2000; Meyer, 1995; Mitro, 1999)

2.  Almost all available winter habitat is in the Box Canyon because macrophytes (rooted aquatic plants) don't provide winter cover, they senesce and disappear in the winter. (Griffith and Smith, 1995; Meyer, 1995).

3.  Higher flows below Island Park Dam lead directly to an increase in the amount of bank habitat, which leads directly to an increase in the number of young trout that survive the winter. (Contor, 1989; Mitro, 1999; Angradi and Contor, 1989)

4.  Putting permanent structures like Christmas trees or “trout hotels” in the river were ineffective because they simply filled up with sediment. Macrophytes do not have that issue because they trap sediment and then release it when they senesce, so it can be flushed away. (Gregory, 2000; Henry’s Fork Foundation Newsletter, Winter 1995)
5.  Physical habitat structure in the Harriman reach during the fishing season is provided by rooted aquatic plants, which increase water depth at a given streamflow rate. Also, all other factors being equal, adult rainbow trout will seek out deeper water. (Kuzniar, Van Kirk, and Snyder, 2017)


  • Angradi, T., and C. Contor.  1989. Henry’s Fork fisheries investigations. Project F-71-R-12, Subproject III, Jobs 7a and 7b. Idaho Department of Fish and Game, Idaho Falls.

  • Contor, C.R. 1989. Diurnal and nocturnal winter habitat utilization by juvenile rainbow trout in the Henry’s Fork of the Snake River, Idaho. Master’s thesis, Idaho State University, Pocatello.

  • Gregory, J.S. (2000), Winter Fisheries Research and Habitat Improvements on the Henry’s Fork of the Snake River. Intermountain Journal of Sciences, 6:232-248.

  • Griffith, J. S. and Smith, R. W. (1995), Failure of Submersed Macrophytes to Provide Cover for Rainbow Trout throughout Their First Winter in the Henrys Fork of the Snake River, Idaho. North American Journal of Fisheries Management, 15: 42-48. doi:10.1577/1548-8675(1995)015<0042:FOSMTP>2.3.CO;2

  • Kuzniar, Z. J., Van Kirk, R. W. and Snyder, E. B. (2017), Seasonal effects of macrophyte growth on rainbow trout habitat availability and selection in a low‐gradient, groundwater‐dominated river. Ecol Freshw Fish, 26: 653-665. doi:10.1111/eff.12309

  • Meyer, K. A. 1995. Experimental evaluation of habitat use and survival of rainbow trout during their first winter in the Henrys Fork of the Snake River, Idaho. Master’s thesis, Idaho State University, Pocatello.

  • Mitro, M. G. 1999. Sampling and analysis techniques and their application for estimating recruitment of juvenile rainbow trout in the Henrys Fork of the Snake River, Idaho. Ph.D. dissertation, Montana State University, Bozeman. 288 pp.

Gill Lice Study

The Idaho Department of Fish and Game and the Henry’s Fork Foundation have launched a study investigating gill lice in the Upper Snake River region after receiving reports of anglers observing gill lice in rainbow trout in the Henry’s Fork. We need your help to gather information on the presence and absence of gill lice.

Help by gathering information and sharing it with us!

Buffalo Fish Ladder: Monitoring the Contribution to Fisheries

As of summer 2013, over 30,000 rainbow trout have migrated upstream through a fish ladder at the Buffalo River Hydroelectric Project. A large number of brook trout, whitefish, and non-game fish species have also used the ladder. There has been a generally increasing trend in use of the fish ladder since it was installed, and the next phase of monitoring will allow us to quantify the contribution of the Buffalo River to the wild trout population in the Henry’s Fork.

The hydroelectric project was relicensed in 2004 and several fish passage improvements were made at the facility in 2005:

  • Upstream-migrating fish benefit from a state-of-the-art, 270-foot-long fish ladder that was designed to allow young rainbow trout to pass over the twelve-foot-high dam. HFF monitors fish moving upstream and downstream through the project.

  • The turbine intake was screened with a smaller opening, and the upstream face of the dam was resurfaced. These changes should prevent fish migrating downstream at the dam from being injured or killed when entering the turbines, or being trapped in holes in the dam.

These fish passage improvements were made to allow juvenile rainbow trout from the Henry’s Fork to access crucial winter habitat. Offspring from spawning rainbow trout in the Buffalo River and juvenile trout migrating from the Henry's Fork are able to spend their first winter in the Buffalo River watershed upstream of the dam. After their first winter, these juvenile trout move to the Henry’s Fork where they can grow and contribute to the fishery from Box Canyon through Harriman State Park.

Project partners and contributors: Caribou-Targhee National Forest, Idaho Department of Fish and Game, and Fall River Rural Electric Cooperative (hydroelectric project owner).

More Information


Long-Term Monitoring

In 1996, HFF began the Habitat Assessment Project, which collected information on aquatic and riparian habitat conditions, fish populations, and aquatic invertebrates on every reach of the Henry’s Fork and most of its tributaries. That project required five years to complete and provided a set of information that could serve as a baseline to compare with future conditions.

In 2000, a set of nine “indicator” sites were selected for long-term monitoring. Six of these are located on the main stem of Henry’s Fork from Mack’s Inn to Rexburg, and one each on three tributaries: Henry’s Lake Outlet, Sheridan Creek, and Fall River. These sites were monitored each year from 2001 through 2005, adding to the data collected during the 1990s. Download the long-term monitoring report from 2005. 

The next round of monitoring is under way, providing a 20-year comparison with data collected during the initial habitat assessment and a 10-year comparison with conditions in 2005. The latest project is the Henry’s Fork water-quality monitoring.

Ecological processes and physical properties of water critical to growth and survival of wild trout are being studied as part of the latest monitoring project. The placement of study sites allows us to identify how water quality changes along the course of the Henry’s Fork as reservoirs, irrigation withdrawal and return-flow points, tributaries, and natural ecological boundaries affect physical, chemical, and biological processes. This knowledge will help river managers to optimize not only water quantity but water quality as well. 

After a successful first year of installing and monitoring four stations along the Henry’s Fork upstream of Ashton Reservoir, HFF expanded its water-quality monitoring network into the lower watershed during the summer of 2015. HFF installed automated instruments (called “sondes”) near Ora Bridge, St. Anthony, and Salem-Parker highway, complementing those installed in 2014 at the Flatrock Club, Island Park Dam, Pinehaven, and Marysville.

The HFF sondes record temperature, dissolved oxygen, depth, dissolved solids, turbidity, chlorophyll, and blue-green algae at 15-minute intervals. At each sonde site, staff regularly collects water samples, which are analyzed for phosphorus and suspended sediment concentrations.

The results from field sampling will be used to develop statistical relationships between constituents that cannot be measured by the sondes and those that can, so that in the future, the sonde data can be used to infer information about a wide range of water-quality parameters.

During 2015, HFF collaborated with several agencies to focus intensive water-quality sampling at Island Park Dam to identify the cause of high-turbidity events observed immediately downstream of the dam each of the past few summers. This study paired a water-quality sonde on the west side of the river with the existing HFF sonde on the east side. In addition, water quality samples were taken at various depths in the reservoir immediately upstream of the dam.

Four more sondes are scheduled for installation in 2016 in tributaries to the Henry’s Fork. The Foundation is pursuing potential partnerships that would allow installation of additional sondes in the Teton River watershed in future years, resulting in a network of a dozen or more stations that will be used to monitor water quality throughout the watershed for the next 20 years or more. 



In 2016, HFF is also working with a graduate student from Indiana University who will be conducting his masters thesis on research related to water-quality in Island Park Reservoir.  You can read a bit more about Jack below.

Jack McLaren

Hello! I'm Jack McLaren. I’m a student at the School of Public and Environmental Affairs at Indiana University, where I am getting two Master’s degrees; one in Public Affairs and one in Environmental Science. For my Master’s thesis I’m conducting a research project with the Royer Laboratory and HFF on how climate change and reservoir age influence water quality in reservoirs and their tailwaters. I’ll be taking a close look at Island Park Reservoir to see if nutrient and sediment levels in the reservoir and its tailwater have changed over time and if there’s any connection with climate change or the age of Island Park dam. I hope my research will be informative for conserving wild trout in the Henry’s Fork River!

I grew up in Denver, Colorado and I love fly-fishing, as well as camping, backpacking, and kayaking in my free time. I am excited to be working with HFF this summer and I hope to see you on the river!


More Information: Island Park Reservoir and water tempertaureIsland Park Reservoir sedimentEnd-of-Season Research Update, and Watershed Integrity Review & Evaluation Project Cover Sheet


Reconnecting Habitat: Fish Passage at Chester Dam

Chester Dam became a barrier to upstream fish passage when it was built in 1938. Chester Dam diverts water from the Henry’s Fork into the Crosscut Canal, which then delivers much of it to the Teton River. The Crosscut Canal was built to deliver water stored in Island Park Reservoir—on the Henry’s Fork—into the Teton River. This allows irrigators on the Teton River to have access to storage water late in the season when Teton River flows drop below what is needed to meet irrigation demand. Chester Dam also diverts water into the Last Chance Canal, which delivers irrigation water to the Egin Bench area west of St. Anthony.

In July of 2008, the Federal Energy Regulatory Commission (FERC) issued a license to hydropower developer Symbiotics of Rigby, Idaho, granting them permission to retrofit Chester Dam with a hydropower generating facility. The licensing and settlement agreement process presented an opportunity to improve fish passage so fish could move up through the dam to habitat above it, as well as improve recreational access.

Improvements include:

  •     Fish screens in both the Cross Cut and the Last Chance canals to keep fish from being lost from the river.

  •     A fish ladder to provide upstream passage to fish habitat above the dam.

  •     A screen on the hydropower turbine intake to prevent large fish from passing through.

  •     Better river access, including improved boat launches above and below the dam and an expanded parking area.

Project partners and contributors: The Henry's Fork Foundation worked closely with Trout Unlimited and the Greater Yellowstone Coalition throughout the licensing process and these organizations are responsible for obtaining the funding for the design and construction of the fish ladder at the project. Other partners include: Idaho Department of Fish and Game, Caribou-Targhee National Forest, U.S. Fish and Wildlife Service, and Idaho Department of Parks and Recreation.


More Information


For more information about the HFF's Science and Technology programs, please e-mail Dr. Rob Van Kirk.