The Big Hole River and its continued state of peril; trout numbers again at historic lows

The Big Hole River’s trout population is still in decline. Conditions appear dire as ever and the worst seems yet to come.

Experts around southwest Montana say that, among the many factors at play, we should be looking at disease and bureaucratic failures as to why the Big Hole is in its continued state of peril.

It’s clear that change – change beyond the stale bickering of outfitters and ranchers within their own echo chambers – is needed.

“Anglers will point to the ranchers with the full ditches and then the ranchers will look at all the fishermen on the river in August,” said Pedro Marques of the Big Hole Watershed Committee. “And we know those arguments, and it’s just not worth (the time). We’ve been having those discussions for 28 years, and they don’t change.”

The Big Hole River hit some of the lowest flows and highest temperatures recorded in modern times in 2021. Some stakeholders believe Montana is experiencing a thirst quench that may come to rival the drought of 1988, when parts of the Upper Big Hole dried up completely. 

With scientists predicting a hotter, drier future, that means less water to go around. And if the Big Hole Valley has one chief lesson for the world, it’s that each drop is precious.   

Recent data from three sections of the 153-mile freestone river in southwest Montana showed the fewest number of brown and rainbow trout since data was first collected in 1969. Counts in 2021 shed a light on the brown trout problem across southwest Montana, but new data also shows a struggling rainbow trout population.

“There is a massive local economy that stands to lose a lot,” said Big Hole River Foundation executive director Brian Wheeler.

Historically, fishing outfitters and ranchers have been at odds with one another when river conditions were subpar, but trout populations would bounce back to some degree. That’s not the case this time around.

Both sides make fair points. Outfitters make their money by taking people fishing, and irrigation is a fundamental part of ranching. Who’s to say who has a right to make a living for their family and who does not?

“Every livelihood depends on it, really,” Marques said.

It’s a highly subjective debate. But here are the facts and trends that local scientists and river watchers know to be true.

After monitoring the Jerry Creek section of the Big Hole – from the Jerry Creek access site to Dewey – Montana Fish, Wildlife and Parks biologist Jim Olsen and his colleagues estimated less than 1,000 brown and rainbow trout per mile.

Counts for rainbow and brown trout were compiled during a recent study of the Hogback section of the Big Hole River. Montana FWP

The Hogback Section of the lower Big Hole is estimated to have between 500 and 700.

The popular Melrose section – which spans roughly from Melrose to Browne’s Bridge near Glen – is estimated to have fewer than 500 brown and rainbow trout per mile.

Counts for rainbow and brown trout were compiled during a recent study of the Melrose section of the Big Hole River. Montana FWP

For perspective, during the early Aughts there were between 3,000-3,500 browns and rainbows per mile through the Jerry Creek section. Hogback boasted over 2,000 as recently as 2013. Melrose peaked at nearly 3,000 at the turn of the century and maintained an estimated 2,500 brown and rainbow trout in 2015.

All three stretches have seen those combined populations plummet after 2017.

Counts for rainbow and brown trout were compiled during a recent study of the Jerry Creek section of the Big Hole River. Montana FWP

1,000 trout per mile through Jerry Creek may not sound too alarming, but Melrose was at that number just four years ago.

Also during these studies, biologists have noted a lack of juvenile fish. If browns and rainbows are failing to reproduce, these numbers are unlikely to improve in the immediate future.

Following back-to-back years of drought, some die off makes logical sense. Less water and warmer water means less dissolved oxygen for the fish. Other rivers are experiencing a similar downward trend but not quite to the same degree.

The tailwater section of the Beaverhead, which had about 1,690 brown trout per mile in 2022, now has an estimated 1,552. The lower portion of the Beaverhead has about 304 browns per mile compared to 426 in 2022.

The Ruby River’s tailwater recently had an estimated 649 brown trout per mile compared to 853 in 2022. There was a slight increase in the lower section of the Ruby with an estimated 257 fish per mile, up from 247 in 2022.

While those data points might not seem overly troubling, Matt Jaeger, hydropower, native species and Beaverhead-Ruby program manager, pointed out that the numbers are still “historically low.” He also suspects there are additional factors at play other than angler abuse, or low flows and subpar habitat resulting from low flows.

“There’s other things that could be contributing to it than just flow,” Jaeger said. “And it appears that there are.”

The Big Hole is the most glaring at the moment.

“We’ve seen declines – nothing on that magnitude of what we’ve seen now,” Olsen said. “But in the past, they’ve really followed water. And so during drought times, populations would decline. But we’re talking a 20 to 25% decline.”

The sharp nosedive we are seeing now, which began in 2017 during good water years, requires a closer look at what could be more complex issues, Olsen said.

The Big Hole River near Divide Bridge.THOM BRIDGE, Independent Record

“Poor water isn’t helping us at all, either, as far as a potential recovery from that,” Olsen said. “We’ve had poor water the last two years, but we were already down in the basement before these bad water years came.”

There’s even a drought management plan already in place along with strict fishing regulations.

So what more can be done? By all accounts, the vast majority of river users are playing by the rules. Given the declining numbers of juvenile trout in addition to the overall population, we won’t be out of the woods for years to come.

Olsen and others speculate some kind of fungal outbreak is possible. The river had such outbreaks in 2014, 2015 and 2017 that killed a “significant” amount of fish. Even when there is not an active outbreak, the fungus is always present.

Based on recent history it’s hard to rule out. There was a confirmed fungal outbreak in 2017, about the time when this recent decline began.

“I don’t know that for sure,” Olsen said of an active outbreak. “But it certainly has been a factor at least in three different cases in the last eight years or so.”

Olsen is awaiting results from a study he requested on a number of dead, seemingly infected, brown trout he came across during the fall of 2022. Since the fish were already dead, it’s not 100% accurate to assume that it was an infection that killed them. Once the cause of death is determined, it can then be compared to what is ailing other infected fish.

One of several seemingly infected brown trout collected from the Big Hole River last fall.Courtesy Photo

“I’m convinced that there’s something going on in the fishery, from a disease standpoint, and frankly, I’m frustrated that the FWP doesn’t have that data,” said Steve Luebeck, vice president of the George Grant Chapter of Trout Unlimited. “I know they collected the samples, but they have not analyzed those samples.”

FWP is not immune to the difficult times our society faces as a whole. Staffing shortages plague many industries, and organizations are being asked to do more with less. Full-time biologists are absorbing the full-time administrative duties of open positions.

The Region 3 Fisheries manager position, which oversees southwest Montana and the Big Hole, has been vacant for about a year and a half. Madison-Gallatin Fisheries biologist Mike Duncan has stepped in as acting manager until the position can be filled.

“Those samples were, I think, going to be included as part of a larger study on potential disease concerns,” Duncan said. “And so unfortunately due to a lack of staffing in the lab, we haven’t been able to get those processed because it takes a pretty specialized pathologist – histopathologist just to analyze those. They haven’t been processed yet.”

Fungus is native and always present in the Big Hole. Fish can naturally fend off dangerous fungi or other parasites if they’re healthy. A stressed brown and rainbow trout population will be more susceptible to outbreaks because fungus is generally a secondary infection, Olsen said.

But why are the fish so stressed? Brown trout especially are known for resiliency and being able to withstand stressors like warm water.

Fishing pressure is probably a knee-jerk response. While harvesting fish caught on the Big Hole is rare, and now heavily restricted, the act of reeling in and handling a panicked trout will leave it stressed once returned to the water.

Angler days have doubled on the Big Hole River since 2008. An angler day translates to one person fishing for one day on the river. In 2008, FWP estimated 60,000 angler days on the Big Hole. Now it’s around 120,000.

Pat Munday, professor of science and technology studies at Montana Tech and author of “Montana’s Last Best River: The Big Hole and Its People,” points out that stress levels in caught and released fish “go off the charts.”

Low water flows aren’t helping. Trout need cold water to survive, and more is better. Ranchers in the Big Hole Valley rely on water from the river to irrigate the hayfields that feed their cattle during the valley’s long winters and are resistant to a federal agency dictating details about withdrawals.

River in Peril: The Big Hole River under threat

Author Pat Munday once referred to the Big Hole River as “Montana’s Last Best River.” And it’s a river that’s threatened by climate change, among other issues.

That’s part of why the Big Hole Watershed Committee was formed. When the Arctic grayling was on the brink of being federally listed as an endangered species, the last thing locals wanted was a government agency fudging with the long-standing water rights.

“When you have someone in Denver or Washington, D.C., making decisions, that doesn’t sit well in western Montana, generally,” Marques said.

Before pulling out your scoreboard and marking down points for the ranchers and outfitters (hopefully we’re past this), you should know there is more to consider.

The time of year when fish are feeling the most stress is important as well. Flows in recent years have been lowest during September and into October, when brown trout are spawning. Fall is also a popular time for fly fishermen to target hungry browns by throwing streamers.

“These low flows going through the brown trout spawn are going to introduce the same kinds of stress levels – high temperatures, low flows – that stress these fish,” Munday said. “If there is disease, it’s going to exacerbate it. Even without disease, it’s going to increase crowding and stress levels as the brown trout are on the reds.”

Butte angler Steve Bryers casts a fly on the Big Hole River near Divide in late June. MICHAEL CAST,

Irrigation can also be observed along the Big Hole past growing season and into the fall.

“Ranchers have this theory of: if they can saturate more moisture into soil in the fall that will give them a boost in the spring,” Munday said.

Increased algae bloom and other nutrients can also increase stress levels. At night, algae growth will consume oxygen because it is not receiving sunlight, robbing trout of precious oxygen which is already at a premium in warm water.

The area above Dickie Bridge known to many as the “dead zone” develops a thick layer of algae during the summer. Munday predicts that this is “increasingly going to be characteristic of the Big Hole generally.”

Interstate 15 crosses the Big Hole River near Glen.THOM BRIDGE, Independent Record

Wheeler has also been monitoring water quality. He’s been compiling data from the entire Big Hole for about three years, from Twin Bridges to Wisdom. His samples have found nutrient pollution, also known as eutrophication.

Wheeler, who is a guide in addition to being the BHRF’s executive director, said that if nutrient pollution was confirmed to be a driving factor in brown and rainbow trout decline, it would explain several issues. Wheeler said it seems nutrient pollution can also exacerbate the effects of Tetracapsuloides bryosalmonae, or T. bryo, which is the cause of proliferative kidney disease (PKD).

In addition to devastating population crashes that can result from PKD outbreaks, Wheeler said through his observations during the last three years it appears that nutrient pollution also negatively affects trout’s respiration, reproduction and growth.

Wheeler and the BHRF have documented elevated levels of nitrogen and phosphorus throughout the river during the past three years.


A common cause for elevated nitrogen levels in Montana, Wheeler said, is agricultural runoff. Naturally occurring phosphorus and phosphorus mines in southwest Montana could explain the elevated phosphorus levels.

“Part of the water quality nutrient issue is also cyclical with lower dissolved oxygen levels,” Munday added. “And again, that correlates with temperature. The warmer water is, the less oxygen can dissolve in it.”

These are theoretically fixable problems so long as they are correctly identified at some point and a plan of action can be put in place by state officials, similar to the reaction to the PKD outbreak on the Yellowstone River in 2016.

“FWP moved with some urgency,” Luebeck said. “They got samples, they got them analyzed, they diagnosed the problem. They fixed it. There does not seem to be the same level of urgency on the Big Hole. They took samples in the river last fall. It’s May. Where’s the data?”

Also similar to the Yellowstone, if the appropriate decisions are made and the ship is righted for Big Hole brown and rainbow trout, the work is not finished. Disease can return, and the river isn’t becoming less popular as a recreation destination or less vital as an irrigation resource.

“And we depend on the State to ensure that a clean and healthful environment is proactively maintained on our behalf, as is explicitly afforded us in the State Constitution,” Wheeler said.

The Big Hole River near Wisdom.THOM BRIDGE, Independent Record

Munday’s main concern is that the large-scale and long-term issue of climate change still looms, regardless of how the current problem is remedied.

“So just as we’ve seen with the impacts on our forest – beetle kill, fires – the EPA predicted significant declines (in Rocky Mountain trout populations) by 2030,” Munday said. “So I think in some ways we’re seeing those kinds of predictions about climate come true.”

Researchers from the University of Montana conducted a study that found declines in Montana’s native bull trout and cutthroat trout were driven by climate change. Bull trout were most affected by reduced habitat, while cutthroat were found to be vulnerable to invasive trout species.

No such study has been published on rainbow and brown trout on Montana. Wheeler said it is “de facto science,” noting summer temperatures, rapidly melting snowpack and severe wildfire seasons.

Munday said an official study is not likely because brown and rainbow trout are not native species, but added a study on the native whitefish could be telling as to what the Big Hole and other rivers are up against.

“Our native fish evolved in this habitat and are a key indicator species,” he said. “Something that’s been just horribly really unprofessional, on the part of Fish, Wildlife and Parks to ignore is collecting long-term data and monitoring whitefish populations.”

FWP Fisheries Division administrator, Eileen Ryce, was not available to comment at the time this story was published.