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Jefferson River Basin waters warming, in trouble new study says [1]
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Date: 2025-07-16
Rivers in southwestern Montana face dangerously high temperatures in summer months, spelling trouble for native trout populations, according to a report presented by Save Wild Trout and Upper Missouri Waterkeeper on Monday night in Helena.
The Jefferson River Basin Abiotic Monitoring 2023–2024 study, produced in part by Kyle Flynn, a scientist and engineer with KF2 Consulting, in partnership with Save Wild Trout, sought to determine the causes why fish have died at an alarming rate in the Jefferson River Basin.
Flynn stressed there are likely multiple factors at play in regards to serious river health issues in the the Big Hole, Jefferson, Beaverhead and Ruby Rivers, but the collected data readings were generally bad.
“Not a great check for any of our rivers,” Flynn said during his presentation.
The study included more than 350 miles of thermal imaging flights via helicopter as well as long-term data collection from in the river itself. The study looked at temperature and oxygen saturation in the water, as well as acidity and streamflow.
Trout in the Jefferson River Basin begin to struggle when water temperatures rise to 70 degrees and an increase to 77 degrees, presenters noted, can kill fish within hours. Necrosis, or when body cells begin to die, has also been observed in some fish.
The report also noted conditions were worse on the Jefferson River in 2024 than they were in 2023, and that that river is of major concern.
“The Jefferson River exhibited the most consistent and widespread exceedances of thermal thresholds of all the systems that were monitored, with many sites surpassing the 25°C (77°F) upper incipient lethal temperature for salmonids, and several sites having water temperature over 26.7°C (80°F) in 2024,” the report states.
However the report also noted that 2024 was unusually hot and dry, “representing near worst-case regulatory assumptions and conditions.”
Even so, the report stated the “available data is of great utility as it provides a compelling argument that thermal and nutrient assimilative capacities in each river are exceeded.”
The study raised additional concerns about the oxygen content of water. Algae blooms have been observed in a number of western Montana rivers and they suck up oxygen, which aquatic plants, as well as fish, need. The report noted instances of oxygen levels in rivers getting extremely low, especially at night when plants most need it.
Flynn previously worked for the Montana Department of Environmental Quality and has taught at Carroll College.
“In the end, we want to take the data and evaluate against certain thresholds that might cause injury to fish or fish health,” Flynn said.
A main reason for the study is to direct protection efforts, stressed Save Wild Trout’s Brian Wheeler and Upper Missouri Waterkeeper executive director Guy Alsentzer during the presentation.
“We can also target and prioritize where and how much we do our restoration efforts,” Alsentzer said. “That has to be done at that macro level, and we have to use the best available science to do it.”
Aerial thermal imaging flights conducted in mid-July of last year showed where the river was hot and where it was not. Combined with data collected from small sensors (occasionally camouflaged to ward off vandalism) the hope is to find areas of respite for aquatic life and protect those.
Data will hopefully be used to help shape policy, Wheeler and Alsentzer said, who also expressed some frustration with state agencies. There are data gaps, they said, and they’re not being filled by different agencies.
“The entire reason that this study is happening is because our state government has failed to do its job to monitor these rivers, and therefore what we are left with is something of a pickle,” Alsentzer said Monday night. “We are left with a dearth of data that now we’re trying to solve and plug those holes.”
Alsentzer also said the Department of Environmental Quality and the legislature were playing “dirty politics” over, “concentrations of nutrients that are allowable in Montana’s rivers,” saying they’re breaking federal law. Water quality laws have been a major point of discussion in the state legislature for the past several sessions.
The DEQ, in a statement, said “non-point source pollution” is the leading cause of water quality issues in Montana.
“The Jefferson River Watershed is no different. Because this type of pollution lacks a single, identifiable source, it requires proactive management,” DEQ spokesperson Madison McGeffers wrote in an email. “The Department of Environmental Quality (DEQ) tackles nonpoint source pollution through programs like its Nonpoint Source Program and partnerships with local watershed groups.”
Additionally, the DEQ statement said the agency is working with the Jefferson River Watershed Council on developing a Watershed Restoration Plan that will allow for increased federal funds through the Environmental Protection Agency.
DEQ has also been involved in the issue in other ways, McGeffers noted.
“Currently, DEQ has developed 91 Total Maximum Daily Loads (TMDLs) ‘pollution diets” for the Big Hole River and its tributaries, targeting pollutants like nutrients and sediment,” McGeffers wrote. “In 2009, DEQ identified riparian restoration as the most effective strategy for reducing sediment, temperature, and nutrient pollution in the upper Big Hole Valley.”
More work by the environmental groups is planned, including nutrient sampling, Flynn wrote in an email on Tuesday. Montana Fish Wildlife and Parks is also in the midst of its own fish mortality study in concert with Montana State.
In a comment on Wednesday, Montana FWP said they are studying the issue.
“These studies look to evaluate all the impacts in the respective systems on fish health from a disease standpoint, fish mortality and what influences it, fish recruitment and survivability to include what’s happening in the tributaries,” Greg Lemon, a division administrator within FWP wrote. “And to also gauge the angling efforts and what impacts that has on fish within the system.”
Additionally, Lemon wrote, FWP said they “welcome” input and feedback from those passionate about Montana’s rivers and that they want to work with a variety of groups.
“In a much broader sense, we believe that tackling issues affecting these rivers is best done in collaboration, including partners like Save Wild Trout and other partners, and that remains our focus,” Lemon wrote.
Wheeler said the hope is the data is helpful to decision makers.
“We want to provide state agencies with data to build that historic record, and we want to give chemical context to the biological issues being faced by the fisheries in the Jefferson Basin right now,” Wheeler said. “And we also want to promote accountability and proper redemptive action when we’re not meeting those thresholds to protect these beneficial uses.”
Jefferson-River-Basin-Abiotic-Monitoring-2023-2024_courtesy-SaveWildTrout
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https://dailymontanan.com/2025/07/16/jefferson-river-basin-waters-warming-in-trouble-new-study-says/
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