The Beaverhead River is at a trickle, and biologist says what it means for trout


The Beaverhead River appears to run green as it flows over algae growing in the shallow water near a fishing access point between Clark Canyon Reservoir and Dillon on Sept. 29.

At a bend in the river before a fishing access point between Dillon and the Clark Canyon Reservoir off the I-15 Frontage Road on the Beaverhead River is filled with algae as the river runs low on Sept. 29 in southwest Montana.

  • Photos by Meagan Thompson, The Montana Standard


The lifeblood of the greater Dillon area flows from the Beaverhead River. The river is managed to produce big brown trout for extraordinary fishing, and supports a core agricultural region essential to Montana’s economy and rural character.

Last week, the upper reaches of the “Beav,” as the river is called by those who love it, dropped to a flow of just 25 cubic feet per second, and will trickle at that rate all through winter.

“It’s not good,” said Matt Jaeger, Montana Fish, Wildlife and Parks fisheries biologist for the Beaverhead. “But it’s not unprecedented.”

Winter flow is determined, above all, by nature.

The Beaverhead is a tailwater of the Clark Canyon Reservoir and its flow is regulated at the dam. Since the dam was built in the 1960s, the amount of water allocated both to irrigation for agriculture and the river has steadily declined at about the same rate, Jaeger said. The decline curved steeply downward in the late 1980s.

The reason: There is less and less water.

“It’s climate change,” Jaeger said. “It’s drought.”

The trickle will impact fish, but Jaeger said there is a silver lining for Beaverhead trout.

And though flow depends foremost on precipitation, a change in reservoir storage policy could provide a little more water for all.


This is one of the worst years of drought in the history of the region, but falls in line with a steady decline in precipitation since the late 1980s.

The Bureau of Reclamation regulates release from the reservoir — both to irrigators and the river. Standing rules governing allocation were determined by a 2006 Environmental Assessment and Finding of No Significant Impact.

The reservoir is currently at 58% of the average from 1981 to 2010, according to the Natural Resources and Conservation Service.

This year’s flow of 25 cubic feet per second is the lowest allowable release into the river, but it’s not the first time the Beaverhead has hit that low.

From 1967 to the present, the average winter release was 167 CFS, and from 1989 to the present, the average was 107 CFS.

A cycle began in the late 1980s — several bad water years interrupted by two or three good water years. That cycle has steadily trended for the worse over time, Jaeger said.

“And that’s repeated itself like three or four times. But every time, that short series of good years has been of lower magnitude, and there haven’t been as many of them,” he said.

From 1990 to 1993, winter release from the dam was at 34 CFS on average. From 2002 to 2009, the average was 31 CFS, and some of those years flow hit 25 CFS. In 2014, flow again reached the allowable low of 25 CFS, and in 2016 hit 30 CFS.

So it’s not unusual in recent years for the river to become a creek in winter.

This year is especially startling, however. In allocation meetings back in the spring, irrigators opted to start a level down from what drought management plans required, Jaeger said.

And in the winter preceding those spring allocations, Jaeger likewise asked for less water in the river than he could have asked for. Those planned sacrifices helped avoid bad flows in the summer, he said, but despite an overall conservative approach, the fierce drought — complete with little rain in the hopeful months of May and June — nonetheless left the river in dire straits by fall.

“We didn’t go into this with guns blazing thinking things were great,” Jaeger said. “Both irrigators and [FWP] were trying to operate conservatively, and we’re in a little better shape than we would have been otherwise.”

To add insult to injury, much of the water that feeds the reservoir comes from the Centennial Mountains on the border of southwest Montana and Idaho, and there’s a year of lag time before that melt makes it through the system, Jaeger said. That means some of the impact experienced this summer is actually a year in the making, and some of the impact of this past low-precipitation winter is still yet to be felt.

Since the late 1980s, the region’s droughts have typically lasted four to six years, Jaeger said. This year is the second in a bad cycle.

“If you look at that part of the past and how it predicts the future, I’d expect that we may not shake this for a few years — if it’s similar to the other droughts in the 90s and 2000s. But, if you want to be optimistic — and on some level why wouldn’t you? — if we get one good winter, it fixes things,” he said.

A National Weather Service report on Sept. 16 gives the region serving the Clark Canyon Reservoir a 40-50% chance of coming in above normal precipitation November through the end of January.

“I think the main thing we can do is just pray for snow. I’m only being partially flippant on that. At the end of the day, that’s what it boils down to,” Jaeger said.

You can’t change the weather, but there may be something else that can be done for the Beaverhead.


In a nutshell, the Clark Canyon Reservoir could theoretically store more water on good years. Space is currently saved to allow for emergency storage during a flood, Jaeger said.

That flood control pool is controlled by the U.S. Army Corps of Engineers, and could be filled to change the reservoir capacity from 174,400 acre-feet to 253,400 acre-feet.

Modeling suggests the difference would allow flows of 50 CFS the worst winters instead of 25 CFS, Jaeger said.

Now, that would only help the first year following a strong year of precipitation, Jaeger said.

“It creates more latitude to borrow from a good year to pay for a bad year,” he said.

In his view, it’s possible policy could change to allow such a thing.

“I think that’s managed very conservatively,” he said of the flood pool. “And I think both the irrigators and the fishery would benefit if, during good years, we can store water in there.”

Jaeger, without speaking for the other agencies involved, said major studies would be required to allow use of the additional storage, including a study of the basin to determine the probability and size of a maximum flood, and a study of whether the dam would safely hold the additional water.

Those studies are expensive, in the realm of hundreds of thousands of dollars, Jaeger said, and the bill would likely fall on the Bureau of Reclamation and the Corps of Engineers.

But unlike theoretical water storage fixes on the neighboring Big Hole River, the infrastructure is already in place to take advantage of.

Conversations between agencies have taken place, Jaeger said, but to his knowledge the necessary studies haven’t been initiated.

“Whether it’s a lack of funding or lack of political will,” he said.

Jaeger said the reserve space is one small part of flood protection for a vast area — the Missouri River floodplain.

“When I said it’s conservative, this is a drop in the bucket compared to things like Canyon Ferry and Fort Peck and Sakakawea and these big mainstem Missouri reservoirs. So we’re not really talking about that much water in the big picture. But it makes a big difference to the Beaverhead,” he said.

The Montana Standard left a message with the Bureau of Reclamation’s Clark Canyon field office Wednesday at noon.


A flow of 25 CFS all winter is not good for trout in general. An ideal release for fish would be more like 200 CFS, Jaeger said. That the trout will have to spawn during such low flows makes matters worse.

Guy Alsentzer, founder of the Upper Missouri Waterkeeper conservation group, was most concerned that the timing coincided with the coming brown trout spawn.

“We’ve had a really hard summer… we should be doing everything we can right now to prioritize viability of a strong younger year class and recruitment of these trout,” he said.

Jaeger said the drop’s timing isn’t unusual. The reduced flow occurred last week and is a matter of transitioning to winter storage as the demand from irrigators slows at the end of the season.

Typically, release is reduced at the end of September or early October. It would be worse if the drop happened in the midst of spawning, Jaeger said. FWP has long worked with the Bureau of Reclamation to set the winter flow in advance of the spawn’s beginning. Browns start spawning on the Beaverhead in early November.

But Alsentzer is right to worry about spawning fish.

Jaeger said the flows will reduce total spawning habitat as the stream banks dry up and riffles get shallow. Fish navigating that habitat will be more vulnerable to stress as they head for redds — fish nests in the gravel.

“Fish are moving from potentially a pretty good distance to find each other, find good habitat, dig redds, fight off competition for mates — all that kind of stuff. You’re making it more difficult, more stressful, and making the fish much more vulnerable to move around when flows are really low,” he said.

Beyond the production of new fish, low flows also hurt the preexisting populations.

“Over-winter discharge is the primary population driver for brown trout in the upper Beaverhead,” Jaeger said.

There, he manages to keep 20% of the browns above 18 inches. This past year, he was at 22%. Doing that generally takes discharges of over 100 CFS for a few consecutive years.

“They go through all the stress of spawning at these really low flows. And when they settle back into a pool that’s kind of small from low over-winter releases, they’re having to compete with a whole bunch of 15 to 16-inch 2-year-old brown trout that are in really good shape,” Jaeger said. “So just from a competition, space and biomass perspective, those older fish are what tends to go away first in these low flow years.”

The brown trout decline across southwest Montana rivers has caused alarm among anglers, outfitters and conservation groups, and prompted the Montana Fish and Wildlife Commission to adopt unprecedented regulation changes. The upper section of the Beaverhead, where most people fish the river, is more the exception than the rule for browns, however.

While sections of just about every southwest Montana river, including the lower Beaverhead, are below 40-year averages for adult brown trout numbers, upper Beaverhead fish counts in 2021 revealed that browns are at 87% of average on the section nearest the Clark Canyon Dam, with browns over 18 inches at 96% of average.

That’s a healthy 1,360 brown trout per mile.

No fish counts were conducted in 2021 at the Pipe Organ Bridge section, a little farther downstream, but in 2020, browns there numbered 130% of average.

“The Beaverhead was one of the few bright spots in the state in terms of both water and the fish population last year,” Jaeger said.

On the one hand, it’s good to have a healthy population and a summer of decent flows going into the winter of frightening low flows, Jaeger said.

On the other, competition within a high density of fish stands to take a toll on the biggest trout, perhaps more so because the population’s top-heavy.


The Montana Fish and Wildlife Commission adopted emergency regulation changes at an August meeting following an outreach effort when working groups were formed, the public was polled for input, and FWP made suggestions.

Exactly how much science went into the changes is debatable, as FWP biologists never indicated catch-and-release and gear restrictions would make a population-scale difference in the rivers affected.

Nonetheless, much of the Big Hole River, from Dickie Bridge down, and the entire Beaverhead River, are now catch-and-release, and restricted to fishing with a single hook on an artificial fly or lure. That includes the upper Beaverhead, where Jaeger said there was no biological basis for the rule change due to healthy populations.

In another rule change, the fishing closure on the upper Beaverhead from the Pipe Organ Bridge to the Clark Canyon Dam was extended, starting on Nov. 1 instead of Nov. 30, to protect browns during spawning. The closure still goes until the third Saturday in May.

That change, Jaeger said, may help the Beaverhead browns.

On the Big Hole, the Melrose section was closed the same dates. The Big Hole browns, however, spawn a month earlier than those on the Beaverhead, Jaeger said.

For just that reason, many outfitters and anglers during scoping said an earlier closing date was necessary on the Big Hole, and recommended a longer section be closed to protect more spawning ground.

In the original FWP proposal made available to the Commission in advance of the meeting, the agency said the same — using a Sept. 30 date and closing a much longer section of the Big Hole for spawning in its preferred alternative.

The FWP proposal was changed the day before the Commission meeting, the date changed to Nov. 1, and only the Melrose section closure recommended in the preferred alternative.

Following the meeting, FWP spokesperson Greg Lemon explained the last-second change to the Montana Standard.

“After several phone calls this week with anglers, outfitters and Commissioners, we decided to make changes to the brown trout regulation proposals,” Lemon said.

“We believe it’s still a good balance between providing protection for wild trout while also providing opportunity,” he added.

In the end, the Commissioners can read FWP’s proposed alternatives and do as they will, as was the case at the August meeting when, following a back-and-forth with FWP fisheries personnel, Commissioners adopted catch-and-release and gear restriction changes.

Certainly, those changes were supported by a significant portion of the public during scoping. However, FWP fisheries officials and even Commissioner Patrick Byorth said they aimed to avoid imposing regulation changes that would affect only a specific groups of anglers — those who use treble hooks and bait — without biological justification.

At the scoping meeting held in Butte earlier in the summer, Jaeger said it was important regulation changes be designed in a way the scientists could learn from. He said the mish-mash of regulation changes resulting from the meeting failed that goal.

“We’re not going to learn which regulations make a difference for brown trout because multiple regulation changes happened in the same reaches,” he said.

What’s more, he’ll have to evaluate the impact of those changes after a miserable winter for trout, because the Beaverhead will be allocated just 25 CFS, day in, day out, all winter.

Can the regulation changes hurt?

“Based on what we’ve learned about these fish populations through time, we expect that the main driver is absolutely going to be flow. So the effects are going to be small relative to flow, whether they’re neutral or positive. I think whether or not they do harm is more of a social question,” Jaeger said.