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The Battle for the Big Hole

Dramatic population declines on some of Montana's most treasured trout streams raise alarms.

The Battle for the Big Hole

The Big Hole River is an environment where agriculture and trout compete for the same resource—water. Here, a barely trickling Wise River flows into the Big Hole. (Jim Klug photo)

Every spring, Montana Fish, Wildlife & Parks (FWP) conducts an electroshocking population survey of the Big Hole River between Jerry Creek Bridge and Browns Bridge. In some years, the river here has more than 2,000 adult trout per mile. On average, the river has about 1,500 trout per mile but the numbers have been dropping in recent years, and the results in 2023 were the worst since they started surveying in 1969, with fewer than 500 trout per mile. The numbers represent a decline of 61 percent over the past decade.

In May 2023, FWP released these grim statistics at a time when anglers were seeing dead, fungus-covered trout carcasses in the shallows; catching still-alive trout with strange lesions, open sores, and moldy rotting fins; and other deformities. Even the whitefish were turning up with S-shaped spines and strange red blotching.

What’s worse, it wasn’t just on the Big Hole. The entire Jefferson River watershed—which includes the Beaverhead, Ruby, and Big Hole rivers—was showing similar signs of decline. Some of Montana’s most iconic and storied trout streams were in trouble, and while there weren’t any concrete answers about what was causing the problems, there was no shortage of speculation. Could it be that ranchers were drawing too much water from the river and/or causing excessive nutrient pollution, or was it fly fishing and recreational fishing pressure that was killing the trout? Beyond all this, climate change was clearly altering the hydrology of the river, not just the temperature, but when the seasonal peaks and low flows occur.

A pale sick-looking trout with fungus and lesions laying on a ruler in a drift boat.
Over the past few years, anglers have been seeing dead, fungus-covered trout carcasses in the shallows, and catching still-alive trout with strange lesions, open sores, and moldy rotting fins; and other deformities. (Wade Fellin/Big Hole Lodge photo)

Wade Fellin, who owns and operates Big Hole Lodge in Wise River, Montana, was one of the first to raise the alarm. He sent a letter to Governor Greg Gianforte on May 30 that was co-signed by more than 30 Montana outfitters, guides, business owners, manufacturers, and nonprofit organizations. The letter requested emergency action to mitigate the damage on the Big Hole and immediately create an inter-agency task force to understand the cause of the problem and solve it. On June 19 the governor wrote back to Fellin’s group promising “FWP has prioritized and will develop and implement additional fish population and health studies on the Big Hole, Beaverhead, and Ruby Rivers and monitor angler use on the Madison and Gallatin Rivers. These efforts will initiate data gathering and will include additional FWP staff, creel clerks, as well as Montana State University professors and graduate students.”

The state also adopted catch-and-release-only and single-barbless-hook-only regulations for highly pressured portions of the Ruby, Beaverhead, and Big Hole.

In August in Wise River, Montana, Gianforte finally met with more than 100 ranchers, guides, and outfitters to hear their thoughts, and also to introduce the community to Dr. Al Zale, a Montana State University (MSU) professor and leader of the Montana Cooperative Fishery Research Unit (MCFRU). The research unit is a collaboration between FWP, MSU, U.S. Geological Survey, and the U.S. Fish & Wildlife Service. Its mission is to conduct fisheries research, educate fishery professionals, and provide technical assistance to fisheries biologists working for state and federal agencies, nonprofits, and industry.

“We’ve worked with FWP on hundreds of projects since our inception in 1963,” said Zale. MCFRU will be working with FWP to conduct four new studies to better understand the problems on the Big Hole and other important Montana fisheries. Zale says the field studies will take three years to complete, with Ph.D. students completing the research in four or five years.

“It’s important to keep in mind that we will be issuing progress reports and providing presentations along the way so people won’t have to wait that long to find out what we’re learning,” says Zale.

An adult mortality study will evaluate the factors influencing trout survival in the Big Hole, Ruby, Beaverhead, and Madison rivers. According to Zale, the adult mortality study will use tagged fish to better understand the impacts of water flows, temperatures, angling activities, and disease.

“We’ll be tagging thousands of fish every year for several years to see the life history of actual fish,” said Zale. We’ll be able to see how many times a fish has been caught, how it was caught, when it was caught, and the life history that helped it survive.”

A second juvenile fish study will concentrate on trout recruitment in the main stem of the Big Hole and its important spawning tributaries. MSU assistant professor Timothy Cline will lead this study and use otolith microchemistry to examine fish movements, age, and geographical origins of juvenile fish. The otoliths (ear bones) of a trout grow over time and build layers of strontium and other chemicals in proportion to the water they live in. By comparing this data, you can tell where the young fish are coming from, discover where the mortality is occurring, and take action to fix the problem.

A separate fish health study will identify fish diseases in the Big Hole, Beaverhead, and Ruby rivers and how they might be impacting the trout populations. FWP also announced a new web portal, sickfish.mt.gov, where the public can report fish-health information.

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According to Communication & Education Division Administrator Greg Lemon, FWP is building greater capacity to study potential fish-killing diseases.

A healthy brown trout being held half in the water, under a fly rod and reel.
At one time, the Big Hole River had more than 2,000 trout per mile, but those numbers have decreased in recent years, and in 2023 dropped below 500 trout per mile. (Ross Purnell photo)

“We know that there is disease already present in the population, these diseases are not uncommon but you often don’t see the impacts until the fish population becomes stressed by other factors,” said Lemon. “What we want to know is if those fish diseases are starting to impact those fish populations more than they have in the past.”

Diseases such as Saprolegnia fungus, PKD, and whirling disease have all been previously identified in Montana.

Lemon says there will be more people in the field on the Big Hole River, and more capacity to respond to reports of sick fish and to take samples more frequently.

“Those who work and recreate on these rivers are troubled by what they see happening to the trout populations,” said FWP Director Dustin Temple.

“FWP is troubled, too, and staff have a plan in place to figure out what’s driving the decline in trout health and abundance. FWP along with private and public partners have a long history of effective conservation work on these rivers. This plan is the first next step toward understanding how those same partners can turn the current circumstance around.”

MCFRU and FWP will also be conducting a recreational use study over the next three years to more accurately determine how much fishing pressure is actually happening on the Madison, Big Hole, and Beaverhead rivers.

Zale says that creel surveys and boat ramp interviews are the traditional methods to quantify the amount of recreational fishing, but they will be looking at new ways to collect the data, including using time-lapse photography, artificial intelligence, and image recognition software to more accurately find out just how much fishing is occurring, and how important it is to the local economy.

Wade Fellin, who along with his father Craig were the first to urge the government into action, wasn’t inspired by the time it took the state to react to the problem, and maintains that while the efforts of FWP and MCFRU are needed, it will take years to get results and take action.

In his original letter he called for an inter-agency task force, and he still believes there are opportunities to come to a solution more quickly.

That’s one role of Save Wild Trout, a nonprofit coalition started by Fellin and others to restore Montana’s coldwater fisheries and the economy supported by rivers like the Beaverhead, Ruby, and the Big Hole.

“Our goal is to find out what can we do more nimbly than the slow-moving barge of government,” said Fellin. “What can we do that is helpful? How can we get more information that is already out there, and do it quickly in a way that will be helpful? We want to be as collaborative as possible, but time isn’t on our side.”

Several men sitting around tables discussing the trout population declines on the Jefferson River drainage in Montana.
Governor Greg Gianforte (with microphone) met with more than 100 ranchers, outfitters, and guides in Wise River, Montana, on August 2 in a public meeting to discuss the diminished trout population on the Big Hole. To his right are Montana State University professor Dr. Al Zale, and Craig and Wade Fellin who own Big Hole River Lodge. (Photo courtesy of Montana.gov)

Fellin says Montana DEQ has approved water-quality data quantifying temperature, and nitrogen and phosphorus pollution in the upper Big Hole watershed. That data has been collected by the Big Hole River Foundation since 2020.

Fellin also believes that the Montana DNRC, Bureau of Land Management, Army Corps of Engineers, Grayling Recovery Project, Bureau of Reclamation, U.S. Department of Agriculture, and several other organizations have data that could aid in puzzling together the cause of plummeting fish stocks.

Save Wild Trout has hired Montana native Kyle Flynn, Ph.D., to bridge the gap between non-governmental and state and federal agencies. Flynn is a professional hydrologist and engineer with an academic and research background in water quality.

As of Aug. 22, Flynn had already installed eight water-quality sensors known as “sondes” in the Big Hole, Beaverhead, Ruby and Jefferson rivers to monitor late-season conditions and discover how water-quality variables might be influencing declining trout populations. Flynn said the sites for the sondes were generally positioned where Montana Fish, Wildlife & Parks regularly conducts fish population estimates.

Save Wild Trout is also pushing for a strict barbless hook regulation across Montana, and is asking anglers to stop fishing when water temperatures reach 68 degrees F. Mandatory “hoot owl” restrictions in Montana kick in when water temperatures reach 73 degrees for three consecutive days.

Fellin says he’s been fortunate his lodge hasn’t received any cancellations due to the dropping fish numbers, and his guests—many of whom booked a year in advance—enjoyed many successful fishing days on the Big Hole in 2023. He says the numbers of trout can rebound very quickly if the problem—and a solution­—is identified quickly.

Paul Mosely, owner of Ruby Springs Lodge on the Ruby River and co-owner of The Complete Fly Fisher on the Big Hole has been fishing the upper Missouri watershed for more than 30 years. He’s grateful that the state is now taking emergency action, but points out that the trout population on the Big Hole has been in decline for many years.

“It’s not like this just fell out of the sky and surprised us,” says Mosely. “We’ve all seen this coming. They have been watching this happen.”

He says the river can’t wait for the results of scientific studies to come in. There needs to be short-term action to save the river. He says the quick fix to all the rivers’ problems is simply more clean, cold water. He believes that more water would alleviate adult trout mortality from disease, improve spawning habitat and results, and provide more sanctuary areas for juveniles.

“I’ve been watching this river for 30 years and it’s easy to see that in big-water years we get better recruitment. If the fish aren’t stressed, they can deal with these diseases. Getting more cold water in the system is the first building block that we can use to get the river back on track.

He suggests buying water rights from the ranches on the Big Hole to return instream flows to the river, and using high-tech monitoring devices to ensure the water they pay for is delivered downstream.

A photo of a blue raft floating on the Big Hole River, with a couple dead trout in the foreground.
Dead and dying trout are showing signs of fungus, strange lesions, and other disorders in Montana's Jefferson River drainage. (Wade Fellin/Big Hole Lodge photo)

Mike Bias, who has a Ph.D. in stream ecology and is executive director of the Fishing Outfitters Association of Montana (FOAM), also believes that lack of water is the cause of the decline.

“Since 2021 and finalized across 2022, U.S. Geological Survey (USGS) has shown a significant direct correlation between reduced stream flow and declining brown trout populations in several rivers across southwest Montana, especially the Big Hole River,” said Bias.

“Under these drastic drought conditions that began in 2019, fish undergo additional stresses of low flows, greater water temperatures, and increased susceptibility to disease. Historically, low flows on the Big Hole typically increased by mid-September, but these drought conditions have been longer in duration, into pre-spawning times for brown trout in late October.”

Interestingly, Western Rivers Conservancy has already been busy buying ranches and water rights in the Big Hole Valley for several years. In 2021 they purchased the 317-acre Clemow Cow Camp property, which has two Big Hole tributary streams flowing through it with 2.77 cfs of water rights. WRC plans to convey the property to the Beaverhead-Deerlodge National Forest, preserve the flows of Cox and Old Tim creeks for the Big Hole in perpetuity, and conserve 154 acres of riparian wetlands and wet-meadow habitat.

WRC also purchased Eagle Rock Ranch along Wise River—a major tributary to the Big Hole. That ranch will also be conveyed to the Beaverhead-Deerlodge National Forest, and water rights to 10.93 cfs of Wise River flow will be managed for the benefit of fish in the Wise and Big Hole rivers. In the wet seasons, WRC will flow their water into the meadows for storage so it seeps into the river later in the year. During the late summer season the water will go directly into the river at a time when the fish need it the most.

In total, Western Rivers Conservancy will be putting a total of 13.70 cfs of critically needed water back into the Big Hole system. The group has a long history of buying agricultural land, preserving it for public use, and dedicating the water rights to the rivers.

To learn more about the crisis in the Jefferson basin, visit savewildtrout.org.


Ross Purnell is the editor and publisher of Fly Fisherman.




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