Missouri River Headwaters Sub-Basin Report – Summer 2021

Executive Summary:
Waterways across Southwest Montana are facing troubling conditions and unprecedented challenges. From an early June heat wave and drought conditions, to historically low fish counts, to our State repealing numeric nutrient standards and allowing reckless pollution into our waterways, our world-class rivers are up against some tough battles this summer. With our rivers and waterways facing multiple whammies of low flows, climate change-induced warming temperatures, increased pressure, development, and pollution, Upper Missouri Waterkeeper is here to keep you in the know on the latest in the Upper Missouri River Basin. We will also be out conducting pollution patrols throughout July and August. Make sure to sign up on our website for updates and if you’re interested in joining.

The Missouri River basin’s water quality is degrading from death by a thousand cuts. Montana Fish, Wildlife & Parks (FWP) has reported a historic decline in brown trout numbers across the state with low juvenile recruitment, but rainbow trout populations are falling in the Big Hole River, and basin-wide rainbows are failing to fill the void. FWP has opened a scoping period to initiate public input through an online survey (here) and three public meetings on various proposals aimed at reducing angling pressure on brown trout, including seasonal closures to protect redds during spawning season, catch and release fishing only, and seasonal hoot-owl restrictions from July 1 thru August 15 from 2 p.m. to midnight. The agency plans to propose restrictions to the Fish and Wildlife Commission during their August meeting.

To top it off, the State of Montana dealt perhaps the largest blow to our waterways this spring when Governor Gianforte unlawfully eliminated science-based numeric nutrient water quality standards, letting the state’s largest polluters off the hook from doing their share to protect Montana’s waterways. Under this new law, Montana’s economic well-being, jobs, and our outdoors heritage are at risk; without clean and healthy rivers, our $7.1 billion outdoor recreation economy and the over 71,000 jobs it supports will suffer, blatantly contradicting Gianforte’s “Comeback Plan.” Instead, our rivers are backsliding and Montana is failing to protect some of the most unique, intact cold water river systems in the Lower 48.

Montana Fish, Wildlife and Parks (FWP) just announced the following additional closures and hoot owl restrictions in addition to the Madison and Ruby Rivers:

  • Beaverhead River hoot owl restrictions from the mouth to Laknar Lane Bridge
  • Lower Big Hole River hoot owl restrictions from the confluence with the Beaverhead River to Notch Bottom FAS
  • Upper Big Hole River full fishing closure from Saginaw Bridge on Skinner Meadow Road to the North Fork Big Hole River
  • Jefferson River entire river hoot owl restrictions

Waterkeeper is going to be out on the river more than ever this summer, patrolling for expected algal blooms, monitoring water quality, and documenting any pollution events. Sign up on our website and follow us on Facebook, Instagram, and Twitter to stay up-to-date on our findings. Please contact us if you’re interested in learning more about how you can participate in this summer’s pollution patrols.

Here’s what we know about the current happenings in the Missouri’s headwaters.

Montana’s Low Water Year:
It’s no secret that snowpack and spring moisture is resulting in historically low flows in many of Montana’s waterways. As mentioned above, the megadrought encapsulating much of Montana and new warmer normals due to climate change will have a multiplier effect on the existing nurtiant and pollution loading we know is occuring. The dewatering of many of these waterways for irrigation and municipal use only adds to the extremely low flows and warming temperatures.

Accordingly, we’ve already seen fish closures on the Rudy and Madison Rivers and historically low flows on the Smith and Jefferson Rivers. A concerning reality that is already occurring at the beginning of the summer before it’s predicted to get even drier and warmer. You can check out NRCS’s basin reports here.


Source: NRCS, accessed June 29, 2021

Gallatin River:
While the Gallatin River is one of Montana’s most cherished and iconic rivers, it’s also become degraded. Pollution pressure continues to grow due to unchecked development throughout the river basin creating unsustainable nutrient loading from existing wastewater and sewage discharges that are amplified in low water years like this one.

FWP hasn’t shocked the Gallatin in several years due to the risks involved with performing a fish count. Although fish numbers are unknown, we do know the Gallatin has exceeded its nutrient pollution tipping point for the last three years, as indicated by unnatural, neon-green noxious algal blooms. With the rest of the basin’s brown trout numbers plummeting, it’s likely the Gallatin is experiencing similar troubling declines.

Severe algal blooms such as the those documented on the Gallatin since 2018 degrade water quality, negatively affecting fish and aquatic life, and are a nuisance to recreationists, caused by excessive nutrient loading, warm water temperatures, and sunlight. In the Upper Gallatin River unnatural nutrient pollution is manmade, caused by irresponsible sprawl development and the disposal of poorly treated wastewater.

Why? New development projects in Big Sky’s Canyon area continue to receive county and state approval to discharge hundreds of thousands of gallons of wastewater that will continue to exacerbate the pollution problems the Gallatin already faces. If state and local officials continue to turn a blindeye to the growing nutrient problem on the Gallatin, Montanans should expect another prolonged algal bloom that could eventually lead to a massive fish die-off or worse. Until the Gallatin has a proven, science-based pollution diet to restore the river to health, new development projects along the Gallatin River should be paused. Stay tuned this summer for more from Waterkeeper.

Madison River:
The Madison River has been off to a rough start in 2021. On May 18th, a fellow river advocate tipped us off to an early season fish kill in the Beartrap section of the Madison. We went out to investigate only to confirm what had been reported to us. All totaled, FWP estimated nearly 1,000 fish, including brown and rainbow trout, and whitefish had been observed dead. Preliminary lab results reported by FWP have been inconclusive and other state agencies tasked with protecting our state’s clean water have been silent. With FWP drifting away from science under the Gianforte administration, will we know the cause of such an early season fish die-off?

Similarly troubling, we were notified of an algal bloom that already broke out on the lower Madison downstream from Blacks Ford and spanning to the confluence of the Jefferson River. UMW went out to investigate, documented the bloom, and notified the state’s water quality division at the Department of Environmental Quality (DEQ).

With water temperatures near Ennis Lake already reaching 70°F in June and flows near Cameron (1370 cfs on June 25, median 2140 cfs) and McAllister (1270 cfs on June 25, median cfs 2400 cfs) well below median values, it’s going to be a long hot summer on the Madison. After a week of water temperatures exceeding 75°F in the lower Madison, hoot owl restrictions are now in place from below Ennis Dam to the confluence with the Jefferson. The restrictions prohibit fishing from 2 pm through midnight each day until August 15 to reduce further fish stress and mortality.

The recently released Madison trout report from FWP paints another grim picture for the future of this valued fishery. Much like fisheries reports on other rivers, brown trout numbers near Norris hit a 20-year low at only 459 per mile, with rainbow trout failing to fill the void as they too were below the 20-year median. Most concerning to biologists was the almost complete lack of 6 to 11 inch brown trout. Without the replacement of juvenile brown trout – often some of the more prolific spawners – the long term future of trophy fish populations in the Madison could be in question.

The Madison River is also one of the most fished in the state. Unfortunately, a plan to manage fishing pressure has been delayed by the FWP Commission. Kicking the can down the road on even small steps won’t sustain this cherished fishery for generations to come.

Big Hole River:
The Big Hole River is often referenced as Montana’s last, best river that holds one of the last remaining populations of native fluvial arctic grayling in the lower 48. While the Big Hole Valley hasn’t yet experienced the dramatic development pressure many of the basin’s other waterways have in the last decade, it has seen fishing pressure grow exponentially in recent years. The river is also experiencing historic declining brown trout numbers.

Brown trout numbers are at an all time low in Melrose – brown trout in 2014 were 1,800 per mile, now are just 400 per mile – with juvenile two year trout also reaching historic lows. Fish biologists found similar declining trends between Jerry Creek and Pennington. Again, without recruitment of younger juvenile brown trout, reversing the decline isn’t likely to happen in the near future, if at all.

While other trout species like rainbow, grayling, and brook trout are not trending as steeply downward, they are also not filling the void brown trout are leaving either. The problem has biologists perplexed as to the cause. Note the survey FWP is conducting and an upcoming Facebook Live event Waterkeeper is co-hosting with Orvis Fly Fishing, Craig Fellin Outfitters & Big Hole Lodge, and Big Hole River Foundation next week on Wednesday.

This summer 2021’s low water flows and warming temperatures, in combination with unhealthy sedimentation, nutrient pollution, and fishing pressure, will magnify local water quality impacts. At last check before the next heat wave that’s expected over the busy Fourth of July weekend, the Big Hole near Melrose was flowing at a paltry 617 CFS, almost 2000 CFS below historic median flows. Water temperatures also spiked to over 70°F on June 23rd. Despite extensive efforts in the Big Hole Valley to increase in-stream flows, it’s still hovering around the 10th percentile.

The Big Hole is also facing increasing speculative, short-sighted oil and gas leasing development pressure that has been stalled for now after Waterkeeper raised alarm bells and helped turn-out thousands of Montanans opposing new fracking in SW Montana’s public lands. But oil and gas leasing in this pristine, fragile ecosystem is still on the table. Industrial oil and gas development in this region’s tough geology would likely require hydraulic fracking, which could be a deathblow to this struggling fishery.

Beaverhead River:
Similar trends in brown trout population level declines have been observed on the Beaverhead. In the last six years, abundance has dropped from 2000 brown trout per mile to 1000 fish. Rainbow trout aren’t faring well either, falling far short of the Upper Beaverhead Management goal of 600 rainbows per mile with only 234 per mile. Again, proportionally few younger fish were observed relative to previous years according to FWP biologists.

Nearly annual pollution events on the Beaverhead River, including toxic blue green algal blooms below Clark Canyon Reservoir, only worsen water quality and habitat conditions for the already stressed trout. With the water runoff season coming to an early end this year, flows near Twin Bridges are approaching the 25th percentile (84 CFS) but are thus far holding around 116 CFS.

Ruby River:
The Ruby was one of the first victims of river closures in Southwest Montana and is now on its second round of closures, prompted by historically low flows. The stretch between Duncan District Road near Twin Bridges and the confluence with the Beaverhead will remain closed to fishing until flows exceed a daily average of 40 cfs for seven consecutive days, or until October 15.

The low flows and heat have also seen temperatures spike to above 80°F in June. It’s best practice to refrain from fishing when water temps reach 68°F and trout begin to show significant signs of stress at 70°F. Increased trout mortality begins to occur at water temps over 73°F.

Like the Beaverhead, over the last 6 years brown trout per mile in the Ruby has dropped from 1500 to only 600-700 in 2021. Matt Jaeger, FWP fisheries biologist for the Beaverhead and Ruby believes catch and release only restrictions won’t have a meaningful impact on trout populations because harvest rates remain low, but restricting fishing during spawning seasons could potentially reduce mortality.

Jefferson River:
Different Southwest Montana river but same sad story. The Jefferson represents the culmination of the Big Hole and Beaverhead rivers and sadly, when it comes to water quality, also represents many of the same water quality and fishery challenges.  The abundance of juvenile brown trout less than 2 years of age is at a 15-year low at fewer than 50 fish per mile in the lower survey section of the Jefferson. Water temperatures have already reached dangerous temperatures for trout viability, peaking at 75°F near Twin Bridges on June 23 while flows have already hit historic lows.

Like the lower Madison, an early benthic algal bloom emerged near Cardwell mid June. Thanks to a fellow river advocate, we were notified of the pollution event and shared the findings with DEQ. Reach out to us if you see something suspicious on the water.


Waterkeeper Pollution Patrols:
This summer 2021, Upper Missouri Waterkeeper will be patrolling the Missouri’s headwaters, collecting water quality data and documenting the scope and severity of pollution, algal blooms, and fish die-offs. We’ve ramped up our sampling methods and recently purchased a YSI meter for measuring dissolved oxygen, conductivity, total chlorophyll and harmful algal blooms, pH, nitrates, and temperature, all of which will be used to build a baseline dataset for water quality across the sub-basin. With the Montana DEQ historically underfunded and under-equipped to consistently monitor the Missouri’s headwaters, much less lacking the political will to take on hard pollution issues, Waterkeeper is stepping up to help fill the void and use science to better document challenges – and solutions – for SW Montana’s waterways.

Because SW Montana’s headwaters are particularly sensitive and vulnerable during the summer season we’ll be regularly patrolling the waters for the next few months. Check out our monitoring schedule and drop us a line if you see something concerning that we should investigate further. Help us spread the word that we’re out on the water and let us know what you’re seeing on the rivers!

Upper Missouri Waterkeeper is the only organization in Montana taking a hard look at the totality of the Upper Missouri River Basin – from Dillon, to Bozeman, to Great Falls. We don’t take corporate polluter money and we aren’t government funded – it’s local clean water advocates that help us protect and improve our headwater streams. Join us today in the fight to protect fishable, swimmable, drinkable water across Montana’s 25,000 sq. mile Upper Missouri River Basin.