Fisheries biologists, others work to identify causes of fish decline in upper Clark Fork River

“Our fish population decline is due to a lack of recruitment,” said Caleb Uerling, a fisheries biologist for Montana Fish, Wildlife & Parks. His territory includes the upper Clark Fork River.

“There’s not juvenile fish growing up to reach big enough size to recruit,” he said.

That’s one piece of a biological jigsaw puzzle begging for assembly, with dozens of contender pieces that ultimately will either fit or won’t.

The question that still looms large is this: Why aren’t juvenile brown trout becoming adult trout in the upper Clark Fork River?

On Nov. 19, Uerling and Nathan Cook, an environmental scientist with the state’s Natural Resource Damage Program, provided a briefing during a Restoration Seminar at Montana Technological University about research underway to try and answer that question, among others. 

The variables bristle thickly, like quills on a porcupine.

Potential cause-and-effect suspects include metals from mining and smelting pollution (copper, cadmium, lead, zinc and arsenic), related impacts to aquatic macroinvertebrates (the bugs fish eat), low flows, warm water, loss of habitat tied to Superfund remediation, changes in pH, conductivity or other measures of water quality, climate change, mortality of young fish in tributaries or spawning challenges there and more. 

“There’s a lot going on in the Clark Fork that’s not great for trout,” Uerling said. “It’s too much to look at all those variables. And so we want to narrow our focus.”

Cook said the Natural Resource Damage Program allocated $1 million to investigate the status of the trout population between the Warm Springs Ponds and Garrison, about 43 miles downstream.

He said a team of people first met in 2022 to brainstorm about the potential causes of the decline and possible remedies. The group included agency scientists, representatives from nonprofits, academics and university students.

Cook said the inquiry has been described as a comprehensive investigation of factors limiting the upper Clark Fork fishery.

“I prefer to call it, ‘Where’s the fish study,’” he said.

The key focus has been the stretch of river just below the Warm Springs Ponds, a reach that once supported nearly 2,000 fish per mile but was recently estimated to support only 25 fish per mile.

Cook noted that the Clark Fork’s headwaters mixes flows from Warm Springs Creek, the Mill-Willow Bypass (which diverts Mill and Willow creeks around the Warm Springs Ponds) and the ponds network itself.

Beginning in 1911, the Anaconda Co. built the first of what became a three-pond system designed to help settle out metals flowing from Butte in Silver Bow Creek. The two subsequent ponds were built in 1916 and 1959.

EPA has estimated the ponds contain sediments and sludges of metals-contaminated materials in volumes great enough to “cover the playing area of 100 football fields 90 feet deep.”

There could be problems in tributaries. Biologists set up contraptions called "screw traps" to capture young fish swimming out of streams like Warm Springs Creek. 

"We did not see many fish come out of those tributaries in the spring of 2025," Uerling said after the presentation.

"We are going to be changing the trapping scheme there next spring to try to confirm that it is truly a lack of out-migrators from those tributaries rather than an issue with the current trap scheme," he said.  

In addition, he said, there will be consideration of young fish migrating out of tributaries in the fall. 

Cook said that Superfund remediation of Silver Bow Creek and the upper Clark Fork, work performed by the Montana Department of Environmental Quality, is reducing the metals pollution in the river.

“But they’re still a source of chronic stress (on aquatic life),” he said.

Cook said the U.S. Geological Survey is examining how the mixing of waters at the headwaters affects biological risks.

“So, last summer, USGS went out and did a synoptic sampling event where they had a small army of people out there collecting water, groundwater and sediments during very slow conditions, and we may repeat that effort in future years,” he said.

During synoptic sampling, samples are collected at multiple locations across a watershed on the same day and within a short time to capture a snapshot of water quality or other environmental conditions.

One variable that has generated vigorous debate is whether the remedial Superfund work along the Clark Fork has ironically played a role in driving the population decline.

During early phases, DEQ contractors adopted a more scorched-earth strategy, removing all streamside vegetation and remaking the riverbanks in ways that removed fish-friendly habitat such as undercut banks. One observer described this strategy as the “Walmart parking lot approach.”

DEQ has since embraced remedial design strategies that are more fish-friendly. The agency has also reduced the scope of cleanup, a change driven in part by concerns the cleanup money will run out before the work ends.

Cook said other research participants are using drones with thermal imagery to map cold spots along the river where trout, a coldwater fish, find refuge when water temperatures rise. Another effort is investigating the viability of spawning habitat.

Meanwhile, Uerling said his personal hypothesis is that water quality is a major contributor to the river’s declining population of brown trout since 2015.

“I think in our ideal world we want to find one variable that’s responsible that we can address, but that’s not likely,” he said. “My hypothesis would be there’s some sort of water quality variable that we’re not understanding that’s responsible.”