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Brown trout decline across southwest Montana rivers
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Brown trout decline across southwest Montana rivers

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Southwest Montana has a brown trout problem.

The species is dropping in numbers across a wide range of the region’s rivers, biologists are stumped as to the cause, and a looming summer of drought is putting on the heat. It’s all hands on deck, and the experts are out for solutions.

“While we try to figure out what's really the root cause of this, we should certainly be doing something. I'm not the decision maker, but that's how I feel based on what's going on biologically — we should be doing something," said Jim Olsen, Montana Fish, Wildlife & Parks fisheries biologist for the Big Hole River.

In the Big Hole’s most popular section, from Melrose to Brownes Bridge, brown trout numbers are the lowest they’ve been in 50 years of surveys. Where there were 1,800 fish per mile in 2014, there are now 400.

In the last six years, the Ruby River has dropped from 1,500 brown trout per mile to historic lows of 600-700 in the upper tail waters. The Beaverhead River has dropped from 2,000 to 1,000.

In the upper Clark Fork’s most historically fishy section near the confluence with Warm Springs Creek, the population of trout over 10 inches has steadily declined since 2013, from 1,800 fish to an all-time low of 82 in 2019.

In the Jefferson River’s lower survey section, brown trout numbers aren’t low overall, but the number of younger, 2-year-old fish is the lowest it’s been in 15 years, at less than 50 fish per mile.

While sportsmen may be on the lookout for big fish, biologists keep special track of the small ones.

Brown trout recruitment — when a fish survives to juvenile size and can be surveyed — has been poor in the last five years in all of the listed rivers.

“It's when we have low numbers of adults and low numbers of little fish. That's where to me the red flag goes up that this is something really to be concerned about,” Olsen said.

Two-year-old fish have reached historic lows in the Melrose section of the Big Hole.

According to Travis Horton, FWP Region 3 fisheries manager, brown trout numbers are below the 20-year average in the Madison River, and recruitment has been poor.

On the upper Yellowstone, Livingston-area FWP biologist Scott Opitz has seen a steady decline in the species. The numbers peaked in the late 80s in the Mill Creek section near Livingston at 700 trout per mile. Since 2016, it’s been between 200 and 300.

What scares the biologists more than the numbers is that they don’t know why it’s happening.

Historically, brown trout responded well immediately following good flow years like 2018 through 2020. Instead of following the trend, the decline is steeper than ever in the last few years. A tried-and-true tell is gone, and mystery remains in its place.

“We're absolutely concerned. When we go to manage these fisheries, it's important we understand what factors are driving the populations — and we had a pretty good handle on that. All of a sudden, something new has come along that we hadn't historically accounted for, because it wasn't there,” said Matt Jaeger, FWP fisheries biologist for the Beaverhead and Ruby rivers.

Many southwest Montana FWP biologists suspect a new regional driver is at play.

“With this kind of stuff, you apply the principles of parsimony. If it's something that's happening over a wide geographic area, and it's affecting different types of fisheries, in terms of how they function hydrologically — free flowing versus impounded — it seems like the most plausible explanation is something that can operate over a large geographic scale,” Jaeger said.

No smoking gun

Each of these rivers is different.

The upper Clark Fork is undergoing serious remediation to clear the river banks of toxic metals from mining, which has in the short term resulted in a lack of the bushy cover brown trout thrive under.

In the Jefferson, severe de-watering for agriculture is always the top population driver, which sets it apart from the Big Hole, said Ron Spoon, FWP fisheries biologist for the Jefferson.

The Ruby and Beaverhead are dammed tailwaters while the Big Hole and Yellowstone are free-flowing.

As diverse as they are, Olsen finds that all the more reason to suspect a greater regional trend is at work.

"The real answer is I don't know. My guess is, given its ubiquitous nature, it's got either something to do with climate or disease. If it was just the Big Hole, we could point at something like fertilizer or some sort of practice that may be occurring only in the Big Hole. But given that these trends are observed in almost all of our local rivers around here, that to me points to something more like that. But that is a guess," he said.

Each known regional factor seems to have a caveat attached, casting doubt on whether it’s the driving cause of decline.

Most of the biologists suspect a changing climate is the root cause. Even disease is often a secondary stressor of changes in temperature and flow, but an exact link between climate and decline still hasn’t been identified.

Water now warms earlier in spring and stays warmer later into the fall, putting pressure on trout. Brown trout, however, are notable for their hardiness and survival in warmer temperatures compared to other species, and the Big Hole has a strict drought management policy in place where area water users adjust their intake when the river is pushed to the limit.

Brown trout are headed upstream in the Big Hole, Olsen said, but while a tagging study from 2008 to 2014 showed the species was more likely to travel upstream than rainbow trout, most tagged fish were caught in the section they started in.

"What our tagging study showed is like 85% of the fish pretty much don't leave their section. Only like 15% of them really kind of move any significant distance. It's probably 1 or 2% that actually go way up the river," Olsen said.

A fungal outbreak caused a significant die-off of Big Hole browns in 2014-2015, and a mountain whitefish die-off in the Yellowstone in 2016.

But Olsen hasn’t observed major fish kills in surveyed sections since.

“If there were significant fish kills you think we would see dead fish. We see some fish with fungus here and there a little bit, but nothing out of the ordinary. The last five or six years we've seen nothing out of the ordinary. Every fall we float the river and look for dead fish. We didn't find a single dead fish the last two years,” he said, adding that it’s much easier to detect big dead fish than smaller ones.

Still, the Big Hole runs for 153 miles, so it’s a huge area to keep track of. Alex Leone, restoration specialist for the Clark Fork Coalition non-profit, pointed to 2019, when copper-laden slickens caused a die-off in the upper Clark Fork near Galen.

“They're super hard to track because the birds usually get them before ... the day after the fish kill we found almost 50. There had been way more before that. And then the next day, they didn't find any. I mean, you just see eagle prints and stuff everywhere," he said.

Angling pressure has dramatically increased across the rivers. All the biologists have seen it. The statewide survey for angling data runs every two years, 2019 being the most recent.

On two popular sections of the Big Hole, angler days have increased from under 30,000 in 2001 to almost 90,000 in 2019.

Harvest data is very limited on the Big Hole.

The aforementioned tagging study showed that 90% of tagged fish were caught and released, but the last creel study to look extensively at harvest was conducted 20 years ago. Creel studies are expensive and labor intensive, Olsen said.

Olsen said he believes based on the existing data and what he’s observed on the river — an angler occasionally keeping one or two fish but never a limit — that no more than 10% of anglers harvest their fish on the river.

If it was a lot more, the fish population wouldn’t survive it, he said.

Regardless, harvest coupled with another cause could still be a factor in the decline, he said.

“That's still 10,000 angler days of people that might be keeping fish. And so that is certainly a concern. And I think it's becoming more popular to keep fish. It used to be very taboo to keep a trout out of a river, and I think more and more people are desiring to eat fish that they catch. And so that is a trend going a different direction than it has in the past. That's my personal feeling on it. We don't have data to back that up, but that's what I think,” he said.

Ron Spoon, FWP biologist for the Jefferson River, said angling pressure is not a driver in the lower Jefferson like it may be on some of the more popular sport-fishing rivers, but harvest data is extremely limited.

“I think we've all come to the conclusion that a lot of people don't tend to harvest their fish,” he said. “But if there's 100 trips out there, on average, how many fish are being removed from that? I have no good information to tell you.”

Spoon said he’s not aware of any new chemical applications being used in local agriculture, but said combined with low flows and high temperatures, chemical inputs in the river could be exacerbated.

“It’s the main reason we probably focus first on looking at flow and temperature, because everything else kind of follows suit with that,” he said.

To indicate just how many factors can affect fish health and how hard they can be to track, Spoon pointed to selenium contamination in Lake Koocanusa in northwest Montana, which stopped fish from reproducing without causing observable die-offs.

“I’m not saying that’s what we have, but there’s a lot of rocks to turn over yet,” Spoon said. “Which is why we are going to try to get together next week and compare notes.”

The biologists from the different rivers are gathering with FWP administration to share data and discuss the brown trout decline next week.

Drought

Why brown trout numbers are suddenly low even in non-drought years is a mystery. As biologists grapple with that question, a drought year is emerging.

The lower Ruby River was closed to fishing near Twin Bridges after falling to a dribble of 8 cubic feet per second last Thursday.

Johnny Kellogg, fishing guide at the Stonefly Inn and Fly Shop in Twin Bridges, reported an immediate decline in the Ruby’s trout population as a result.

“They got hammered by eagles and ospreys. They were just having a day on them,” he said.

Jaeger said the closure doesn’t bode well.

“We don’t have the snowpack. There’s almost no mid-elevation snow. And I think it’s pretty well chronicled how especially southwest Montana is faring in terms of drought” Jaeger said.

Usually mid- and low-elevation snow would feed the Ruby Reservoir which feeds the river, and melt from the Tobacco Roots would feed the stream by tributary.

“The flow just hasn’t been there this year,” Jaeger said. “As a result of that, it's been a real challenge for the dam owners to split water between in-stream flows and irrigation. It's awful dry right now. And folks need to start irrigating. So it's a really challenging job.”

According to U.S. Geological Survey data, the Big Hole, a free-flow stream, was running at about 2,000 cubic feet per second with a water temperature of 58 degrees through Melrose on Tuesday. The average flow that day for the last 100 years was 3,460, and the average temperature on that day since 1995 was 51 degrees.

The Jefferson is flowing at about 50% of normal.

While its flow is closer to normal, 1,650 cubic feet per second compared to 1,900, the Madison River’s water temperature near McAllister was at 60 degrees on Tuesday. Since 1976, the average for that day of the year was 54 degrees.

Current drought conditions will be taken into consideration as the FWP confronts the fish decline, Jaeger said.

“It’s definitely going to factor in the decision making — no question,” he said.

Response

In a recent presentation to the George Grant chapter of Trout Unlimited, Olsen listed off tools in the bag to protect the Big Hole’s brown trout in decline.

Possible regulation changes included switching to catch and release on the river and seasonal closures to protect sections of the river during the brown’s fall spawning and winter egg incubation period.

“While you're not catching the fish, you can you can step on the redds and affect the survival of those eggs. They're very sensitive to disturbance through the first half of their incubation period in particular,” Olsen said.

Jaeger said harvest isn’t high enough on the Ruby and Beaverhead for a switch to catch and release to have a meaningful impact on fish, but restricting the spawning season could.

“That's when they're already stressed out and they're vulnerable to mortality. If folks are catching them when they're in that state, it's a way, way higher chance that those fish are going to die just from being caught and released,” he said.

Sections of the Beaverhead maintain winter closures for precisely that reason, he said.

Habitat projects have made a significant difference to the population over the years. The lower Pennington section of the Big Hole, which has less brown trout density than the upper sections, has nonetheless held its own as the other sections declined. Olsen attributes part of the success to the habitat projects.

There are more dramatic changes available to help trout as well, Olsen said, specifically projects that would put more cold tributary water in the stream in exchange for warmer river water. These projects involve the cooperation of water users and the manipulation of water rights — no fast process in the state.

Spoon has achieved one such project on the Jefferson, Olsen noted.

“If a fish biologist was the king of the world, that's what we'd be working on,” he said.

On the more extreme end of conservation efforts would be building cold water storage with a dam. George Grant Trout Unlimited member Dr. Paul Siddoway has been pushing for such a project on a Big Hole tributary for a long time. He’s a keeper of the river, heavily involved in its conservation, and a respected doctor in the Butte community.

Of course, the project would be expensive, complicated, and building dams in the current political climate is a tough sell, both Olsen and Siddoway said.

Siddoway said the trout are more than worth it regardless. He has also long called for closure of reaches of the Big Hole for spawning, and a move to catch and release.

Olsen said the data didn’t suggest the urgency before, but the mysterious decline has changed that.

For his part, Siddoway believes FWP can’t act fast enough on the regulations.

“I don't think there's any doubt whatsoever that changes need to happen. Soon. I can't think of any reason why we wouldn't attempt to save this population. It's like somebody coming to my office and saying, oh, guess what, your health is declining, but we're going to wait till next year and see where it's at without doing anything," he said.

Normally, emergency regulations are proposed in August so they can go into effect the following year, and the general fishing regulations are reviewed every four years.

Whether something could happen sooner would depend on a number of things — the recommendations of the biologists and the feasibility of making a difference with changes in the regulations, as well as the feasibility in implementing them, said FWP spokesperson Greg Lemon.

But, by way of an emergency decision of the Montana Fish and Wildlife Commission, short-term regulation changes to respond to the brown trout decline is possible, he said.

He said a change in walleye fishing limits for Canyon Ferry Lake and the closure of the lower Ruby this year are examples of fast emergency changes.

“The question is should we do it?” he said, adding that changing fishing regulations mid-season is very complicated logistically.

In the meantime, FWP has taken action with a major research project aimed to figure out where brown trout are declining and why.

The project lead, David Schmetterling, is working with all the state’s brown trout data, FWP colleagues and USGS personnel, to try to identify trends that tell the story of the decline.

Ironically, before that he was studying the expansion of the species’ range in the state.

“What we've been able to find is that expansion is the result of our changing climate. Simply the changing and the timing and duration of spring snowmelt run-off and also gradually increasing temperatures in general. So what was once inhospitable habitat for brown trout is now becoming hospitable to them,” he said.

Now he’s using data for 40 sections of 14 rivers across Montana from 1980 to 2020.

He’s detected an overall decline in brown trout from rivers in the state since 2000, he said, and is now looking at the bigger picture in flow and population to identify broad patterns within the decline.

“We are really concerned about it. We're performing these analyses so we can get an understanding of what's contributing to these declines,” he said.

Whatever longer story of decline he discovers, Schmetterling said local impacts on the species should not be taken lightly.

“Local impacts could be more significant,” he said.

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