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Rainbow Trout Suppression on the South Fork of the Snake River

Rainbow Trout Suppression on the South Fork of the Snake River
The South Fork of the Snake is one of the best tailwater fisheries in the West. It became famous for its outstanding dry-fly fishing for Yellowstone cutthroat trout, but nonnative rainbows have become more populous in recent years. Photo: Arian Stevens

This article was originally titled "Shocking Developments: Rainbow Trout Suppression on the South Fork of the Snake River". It appeared in the June-July 2020 issue of Fly Fisherman.

An Evinrude-powered jet sled slowly prowls a long pool on the South Fork of the Snake River. The olive-jacketed passengers sport caps emblazoned with the shield of Idaho Fish & Game. Two of them use long-handled nets to capture belly-up fish that have just been stunned by electric currents emanating from a powerful battery pack aboard the boat. The electroshocking is harmless. If the trout aren’t netted quickly, they regain their senses and flee to deeper water.

The fish that do end up in the net—cutthroat, browns, and rainbows—are measured, and these stats are recorded before the crew moves to new water, where they repeat the process again and again. This type of activity is used on rivers across the country to measure the health of fisheries and overall abundance, but in the spring on the South Fork, Idaho Fish & Game targets spawning beds used by nonnative rainbow trout. The rainbows are not released back to the river. They are placed in containers and trucked to other waters in the state, where they are unlikely to hybridize or compete with native cutthroat trout. It is a dramatic twist in a 15-year suppression program that so far has failed to reduce the relative abundance of rainbow trout in the South Fork.

The push for native trout preservation is at the forefront of fisheries management in the West. Major efforts are underway in Colorado and Montana to safeguard greenback and westslope cutthroat populations, respectively. Montana and Idaho are protecting dwindling numbers of bull trout. In Yellowstone National Park, small streams like the Upper Gibbon and East Fork Specimen Creek, and lakes like High Lake have been poisoned to remove invasive brook trout. In Yellowstone Lake the National Park Service has been using gillnets to remove lake trout. In some of these locales, nonnative trout have been long established. In others, their presence in substantial numbers is a recent phenomenon. Idaho’s South Fork of the Snake River falls into the latter category.

The Rainbow Dilemma

Palisades Dam on the South Fork of the Snake was completed in 1957, and since that time, the big tailwater in southeastern Idaho has drawn tens of thousands of anglers annually. Fly fishers flock to the river for its exceptional dry-fly fishing and large numbers of trout. Population estimates in the 1980s boasted over 4,000 cutthroat per mile, and back then, rainbow trout made up just a smidgen of the total trout abundance. Despite previous decades of heavy stocking, rainbow trout found it difficult to gain a toehold.

Things changed in the late 1990s. After two years of record flooding and runoff, the abundance of rainbow trout and cuttbow hybrids rose steadily. By 2003, it achieved near parity with native Yellowstone cutthroat trout. The situation aroused alarm in the region. Idaho was concerned most about the possible listing of South Fork cutthroat under the Endanger Species Act which, in turn, could result in a limited fishing season and curtailment of long-standing water management practices in the state. Anglers worried that one of the most cherished cutthroat rivers in the world would lose its native fish.

Yellowstone cutthroat trout have disappeared from much of their native range due to interbreeding with rainbows. Photo: Arian Stevens

To counter this trend, Idaho Fish & Game (IDFG) developed a three-pronged strategy in 2004, including the establishment of weirs on tributaries to prevent rainbows from accessing cutthroat spawning grounds, timed releases from Palisades Dam to scour rainbow spawning beds on the main river, and a controversial change in regulations allowing unlimited harvesting of all rainbow and cuttbow hybrids.

It was a bold management plan that faced significant limitations. Flows of 25,000 cubic feet per second (cfs) from the dam were needed to sufficiently impact rainbow spawning. This tactic was considered the most effective way to reduce rainbow numbers. Such levels, however, are almost impossible to achieve due to irrigation demands and potential flooding. Weirs have proven successful at preventing rainbows from reaching tributary spawning grounds, but they do nothing to limit the even greater spawning activity that occurs in the main river. And while research suggests angler harvest may be the most efficient method for controlling rainbows, it has always been a contentious issue. Most catch-and-release fly fishers continue to release their rainbows.

Despite all these shortcomings, the strategy showed early signs of success. While rainbow trout numbers remained strong, they rarely exceeded 2,000 trout per mile. The rainbow trout population was static, and cutthroat trout were at least holding their own.

But in 2018, electroshock data produced disturbing results. Rainbow abundance had surged to over 3,000 per mile, while cutthroat had plummeted to under 1,900 per mile.

A New Plan of Action

Facing the continued deterioration of a native fishery, IDFG considered removing rainbows and cuttbow hybrids during its annual autumn electroshock survey. “We initially considered this tactic in 2004,” said Brett High, upper Snake River fisheries manager. “But our office faced a lot of pushback. We were told in meetings throughout the area that if rainbows were to be removed, they (the fishing public) wanted to be the ones to do it.” More than 15 years later, it became obvious that angler harvest couldn’t get the job done, and removal via shocking emerged as a potential savior.

Shocking seems easy. Running electric currents through the water brings up heavy numbers of stunned fish in the immediate area. Most who see it are quickly impressed by its effectiveness, but there are constraints.


Electroshocking in stable fall water conditions has been used for many years as a means to quantify trout populations in the South Fork. The same tools are now being used in the spring to gather rainbow trout from their spawning beds and remove them from the river. Photo courtesy of Idaho fish & game

Electroshock population surveys on the South Fork normally occur in late autumn, when river levels are low and current speeds minimal. These conditions produce the best results. Data reliability comes from surveying the same reach every year in similar water conditions. In the case of the South Fork, data from the upper river—where the rainbow population is greatest—is collected from a 2.5-mile section. This leaves dozens of miles untouched by IDFG.

Spring electroshocking theoretically allows IDFG to target spawning beds where thousands of rainbows collect in specific parts of the riverbed. However, in the spring, runoff and increased releases from Palisades Reservoir create higher flows and deeper water. These conditions limit the effectiveness of electrical currents.

Timing is also an issue. South Fork rainbows typically spawn for no more than a month before cutthroat begin the same process in many of the same areas.

In the end, IDFG determined an “all-hands-on-deck” approach was needed. With limited additional financial support—$7,000 on top of their annual fall electroshock survey funds—IDFG attempted electroshocking in both seasons.

In mid-April of 2019, a skeleton crew of IDFG officials in a single jet sled cruised the upper South Fork to target specific beds for a trial run of 19 days over a four-week period. Their goal was 3,000 rainbow and cuttbow hybrids. A total of 5,857 were removed. That might seem like a lot of fish, but it is a drop in the bucket when considering the 2018 survey results of over 3,000 rainbows per mile on the upper river. Nonetheless, when considering the time and personnel limitations of this initial run, the results were encouraging. IDFG plans to double its efforts in 2020.

What to do with the trout after they are removed has been a topic of hot debate. Currently the trout are moved to holding ponds throughout southeast Idaho that are used for youth fishing programs. Some people want them stocked in waters where rainbow trout dominate and have a long history, like the Henry’s Fork or the main stem of the Snake River below Idaho Falls. These are all future possibilities, pending public comment and precautions to mitigate disease transmission and impacts on resident fish.

Removal will continue in the autumn during the annual electroshock survey, but spring spawning season will be the focus. “Sure, it’s a lot tougher work in spring,” says fisheries biologist Patrick Kennedy, “but we found our method of shocking to produce well. Targeting concentrated fish has its advantages. We capture a lot of rainbows before many of them actually spawn. This will impact their abundance over the coming years.”

The department is not abandoning their three original approaches. Harvest is still being encouraged, and tributary weirs will remain for the conceivable future. And while it is unlikely that the dam releases required to scour rainbow spawning beds will ever occur, IDFG is working with the Bureau of Reclamation to better guarantee flows from Palisades Dam that benefit Yellowstone cutthroat the rest of the year. Winter is a major focus, when higher flows can be conducive to the survival and development of juvenile cutthroat.

What the Future Holds

Data from the fall 2019 survey indicates spring electroshocking had a positive impact. Results show an increase in cutthroat abundance and a substantial decline of rainbow and cuttbow numbers of over 800 per mile. But this is one year, and a review of previous surveys shows a wide level of inconsistency from year to year. Still, IDFG, conservation organizations like Trout Unlimited, the South Fork Initiative (a division of the Henry’s Fork Foundation), and a large segment of the fishing public are hopeful this new strategy might turn the tide in favor of native dominance.

The stated goal of the IDFG management plan is to 1) protect the genetic integrity of native Yellowstone cutthroat, and 2) reduce rainbow and cuttbow numbers to pre-1990 levels, roughly 10% or less of total trout abundance. Rob Parkins, public waters access coordinator for Backcountry Hunters and Anglers (BHA), believes these objectives are attainable and, more importantly, will lead to a river with as robust a trout population as it has now. “Some will tell you removing 5,800 rainbow trout results in fewer fish on the South Fork,” he says. “All the science I have reviewed says those fish will be replaced by cutthroat, and probably within a year.”

“Opportunity is a key issue here,” Parkins adds. “BHA supports these efforts because a stable population of cutthroat means increased opportunity to catch a trout native to its waters. You can’t do that most places in Rocky Mountain states.”

Regardless of arguments for and against removal of rainbows, success depends on a number of factors, not least of which is continued public support. IDFG feels this support remains strong. The only question is, which tactics the public is willing to support and, as the lack of participation in harvesting indicates, take part in.

IDFG is also considering additional measures. Mandatory kill regulations is one option. This approach is considered extreme by many and unlikely to garner public backing. New technologies that target juvenile rainbows and rainbow eggs are another possibility. “Innovative methods are always popping up in fisheries management,” Kennedy says. “We just don’t know what tools might be available a few years from now.”

*Boots Allen is a fly-fishing guide and writer who lives with his wife and two kids in Victor, Idaho. His latest book is Finding Trout in All Conditions (West Margin Press, 2016).

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