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Enviro Groups Petition DEQ to Limit Nutrient Pollution on Big Hole River

Petitioners say pollution-related algal blooms threatening Big Hole’s famed trout fishery

Algae blooms along the Mudd Creek Bridge portion of the Big Hole River, which has seen a sharp drop in its trout population in recent years. Photo by Brian Wheeler
Algae blooms along the Mudd Creek Bridge portion of the Big Hole River, which has seen a sharp drop in its trout population in recent years. Photo by Brian Wheeler
by Amanda Eggert, Montana Free Press

Two conservation groups are petitioning the Montana Department of Environmental Quality to designate the Big Hole River, a treasured southwestern Montana fishery, as impaired for nutrient pollution.

The groups argue that an impairment designation will lead the state to put the Big Hole on a “pollution diet” to limit the nitrogen and phosphorous that are contributing to the fishery-damaging algal blooms that have become a recurrent issue.

Common sources of nutrient pollution can include runoff from fertilizers, insecticides and herbicides as well as poorly maintained septic systems and manure from livestock.

Upper Missouri Waterkeeper and the Big Hole River Foundation are basing their petition on five years of data collection that has found consistently high levels of nitrogen and phosphorus at multiple sites on the Big Hole. The groups also incorporated a macroinvertebrat, or bug, study and an overview of the state and federal laws governing the beneficial uses of waterways in their petition.

“There’s no disputing that there’s a nutrient pollution problem on the Big Hole River, with neon-green algal blooms fueled by nutrients cropping up each summer,” Upper Missouri Waterkeeper Executive Director Guy Alsentzer wrote in a release Wednesday about the petition. “Thankfully, the State of Montana has the tools to restore rivers impaired by nutrients, like the Big Hole. We now need to hold the State accountable for taking the necessary steps to designate the river as impaired, develop a pollution diet, and work to reduce pollutant sources that are causing degradation.”

Overgrown algae can depress dissolved oxygen levels, harming fish and some of the macroinvertebrates they eat. In some areas, an increase in algae is linked to reduced biodiversity and diminished ecological resilience.
“The Big Hole is suffering blow after blow — extremely low flows prompting mid-season fishing closures, and miles-long algal blooms,”  – Wade Fellin, Program Director, Save Wild Trout
The petitioners would like the DEQ to acknowledge that portions of the Big Hole are exceeding established water quality thresholds, recognize they “are not fully attaining their aquatic life or recreational uses” and designate the waterway as impaired for nutrient pollution. The petition also notes the historically low flows, high water temperatures, and declining fish populations the Big Hole has seen in recent years. 

The 32-page petition comes as anglers and researchers attempt to understand the factors contributing to a marked decline of trout populations in a handful of cold-water fisheries in the Jefferson Basin. 

In 2023, FWP biologists recorded historically low numbers of brown trout along some stretches of the Big Hole. Anglers and conservationists floated a number of possibilities that may be contributing to the decline, ranging from pathogens and drought conditions to angling pressure and unmitigated pollution. Save Wild Trout, a nonprofit formed in 2023 to understand which factors merit further investigation, has described the 2023 southwestern Montana fishery “collapse” as a “canary in the coal mine moment.”
The East Bank Fishing Access Site located along an upper stretch of the Big Hole River, an undammed river in a largely undeveloped region of southwestern Montana. Photo by Wade Fellin
The East Bank Fishing Access Site located along an upper stretch of the Big Hole River, an undammed river in a largely undeveloped region of southwestern Montana. Photo by Wade Fellin
Wade Fellin, a longtime fishing guide who serves as Save Wild Trout’s program director, described the impairment designation petition as part of his group’s larger effort to help the Big Hole recover from chronic and acute threats.

“The Big Hole is suffering blow after blow — extremely low flows prompting mid-season fishing closures, and miles-long algal blooms,” Fellin said in the release. “We must do what we can now to make measurable improvements for the river, and that should start with an official impairment determination to clean up the nutrient pollution that is degrading water quality and aquatic habitat.”

A spokesperson for DEQ wrote in an email to MTFP on Wednesday that “nutrient conditions and other algae growth factors appear to be at levels conducive for algae growth in the Big Hole River and several of its tributaries.”

The agencies noted that it has been monitoring algae levels on the Big Hole since 2020 and that streamflows and temperatures play an important role in both overall fishery health and algae growth.

Under existing law, DEQ is required to provide an initial determination on the petition within 60 days, although Montana lawmakers are debating a bill by House Majority Leader Steve Fitzpatrick, R-Great Falls, that would stretch the agency’s response time to 180 days. House Bill 684 passed through the House last month and cleared an initial Senate vote on Wednesday.

In response to the 2023 population slump, Gov. Greg Gianforte announced the launch of a multi-year research effort on Jefferson Basin rivers that Montana Fish, Wildlife and Parks is coordinating with Montana State University.

Researchers are just embarking on the second year of that research, which will continue for at least three years, according to FWP spokesperson Morgan Jacobsen. 

One component of that research is examining how flows, water temperature, angling and disease may be contributing to adult fish mortality. A second prong will evaluate tributaries' contribution to the recruitment of juvenile fish into the adult population. Finally, FWP is examining disease threats with the hope of developing a way to proactively support fish health. 

To facilitate that research, biologists have tagged trout in the Big Hole, Ruby, Beaverhead and Madison Rivers. FWP is asking anglers who catch a tagged trout to fill out a report online to aid researchers.

Last year, biologists noted improved population counts for brown and rainbow trout on the Big Hole compared to 2023. Both species are still generally down from 15-year averages. Jacobsen said the 2025 counts are currently underway and estimated that data from those surveys should be available in about a month.

This story was originally published by Montana Free Press at montanafreepress.org.
Amanda Eggert
About Amanda Eggert

Amanda Eggert studied print journalism at the University of Montana. After four years working with the Forest Service as a wildland firefighter, she worked for Outside magazine as an editorial fellow before joining Outlaw Partners’ staff to lead coverage for Explore Big Sky newspaper and contribute writing and editing to Explore Yellowstone and Mountain Outlaw magazines. Prior to joining Montana Free Press’ staff in 2021 Amanda was a freelance writer, researcher and interviewer.
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