Upper Clark Fork brown trout fishery: 'Almost a complete loss'

The trio prepared to fish the Clark Fork River downstream of the mouth of Warm Springs Creek. Two were old friends given to swapping insults. 

After they waded into the river and began casting, a blizzard hatch of caddis flies emerged. Brown trout rose, one after another, a treat for eye and ear.

One man started to regale his friend about a previous fishing outing but stopped mid-sentence to spit and sputter. 

“I swallowed a caddis fly,” he croaked. “I guess that’s what happens when you tell lies.”

His friend quipped, “You must have a belly full of them.”

In those days, during the early 1990s, the upper Clark Fork River had a reputation for lively catch-and-release fishing for brown trout, known to be more tolerant of imperfect habitat conditions than other salmonids.

Population estimates by Montana Fish, Wildlife & Parks suggest brown trout numbers in the vicinity of a pH shack downstream of the inflow from the Warm Spring Ponds were as high as 2,500 fish per mile throughout much of the 1980s.

Starting in 2015, densities declined to an average of about 200 fish per mile.

What happened?

The fisheries task last week required sinew, savvy and an occasional whack with a steel mallet.

The day’s goal was deployment in the Clark Fork River’s uppermost reaches of a cumbersome “rotary screw trap.” Idaho Fish and Game has described the traps as car-sized.

The mechanism’s cone, trap box and pontoons direct flow to trap juvenile fish swimming downstream.

Most of the young fish, likely progeny from brown trout spawning upstream, will be measured and weighed before being released. A few will be captured and caged for a mortality study. The screw trap will also capture older brown trout and other fish species, but young brown trout are the focus.

This field research endeavor is but one of many underway as part of a $1 million multi-faceted investigation into what happened to a once abundant population of brown trout in the upper river.

“The trap will help us understand how many juveniles are coming out of Millow-Willow Bypass and Warm Springs Creek,” said Caleb Uerling, a fisheries biologist for Montana Fish, Wildlife & Parks.

Uerling and FWP colleagues Savannah Johnston, Tracy Elam and Robert Clark toiled on March 26 to install the trap. It was a clear, calm day at the river’s headwaters near Warm Springs. Nature’s accompaniment included the “conk-a-lee” song of male red-winged blackbirds and the honks of Canada geese. A bald eagle flew overhead; its talons had reduced the trout population by one.  

The study underway hopes to reach into a thorny buffaloberry thicket and emerge with a few answers.

There is little hope of identifying a single smoking gun. That’s because the upper Clark Fork River is a remarkably complex system, one beset by more than a century of historic mining and smelting pollution and vulnerable more recently, ironically, to the impacts of remediating rather than contamination.

The potential contributors to a population decline include a dizzying array of variables that likely interact.  

Nathan Cook, formerly a fisheries mitigation biologist for FWP, now works as an environmental scientist with the state’s Natural Resource Damage Program, or NRDP.

At first, biologists concerned about trout population declines in the upper river hoped the fish had simply relocated downstream.

“FWP started looking into the low fish numbers in 2015,” Cook said. “They noticed fish numbers were way down and started electrofishing sections of the river they typically do not sample every year.

“The hope was that they would find the missing fish,” he said. “They did not. In fact, they observed that fish numbers were low everywhere upstream of Deer Lodge.”

Fish numbers between Deer Lodge and the Warm Springs Ponds reached a 50-year low in 2023.

One inescapable variable is the Superfund cleanup underway in the upper river. The Montana Department of Environmental Quality is shepherding the remediation and is working with NRDP to coordinate remediation with resource restoration. EPA has oversight. Money for DEQ cleanup and NRDP restoration came from a settlement with Atlantic Richfield/BP, the corporation deemed responsible for cleanup because it purchased the original polluter, the Anaconda Co., in 1977.  

Some cleanup phases have been more aggressive than others, removing virtually all streamside vegetation and often otherwise degrading trout habitat by removing undercut banks where fish find shelter.

The bureaucratic phrase for this approach is “habitat simplification.”

The cleanup has addressed mining and smelting pollution in the floodplain and riverbanks. Contaminants include arsenic, cadmium, copper, lead and zinc. Copper is an essential nutrient at low concentrations but is toxic to aquatic life at higher concentrations.

The upper Clark Fork River gets low and warm in summer, partly because of water withdrawn for irrigation. Climate change is in the mix.

In addition, people wonder whether outflow from the Warm Springs Ponds network, constructed during the last century to capture contaminants flowing down Silver Bow Creek, differs in water quality from years past.

In short, the effort to identify the primary culprits linked to the fish population’s plummet is akin to a vertigo-inducing game of pin the tail on the donkey.

NRDP funded the trout study.

“Since 2024, when the $1 million was allocated, we have developed a specific plan to expand FWP’s fish research, expand water quality monitoring [by the U.S. Geological Survey] and evaluate fish habitat,” Cook said.  

“The water quality data as a whole show things are improving in the upper Clark Fork River,” he said. “Metals and nutrients have gone down. But the trout population is not responding and there are lots of us out there trying to figure out why.”

Phase One of the Clark Fork River remediation work was completed in 2014. Willows planted during that work are growing.

Given the complex and momentous task of river remediation, is it unrealistic to believe an ecosystem conducive to coldwater fish like trout would bounce back in a bit more than a decade? Maybe a healthy aquatic environment in the upper Clark Fork is still decades away. 

Cook shared his thoughts.

“I do think patience is warranted when setting expectations for a restoration project at this scale,” he said. “It takes a long time for vegetation to mature and the river to adjust. Especially when thinking about habitat and vegetation, we need to have a long-term view of things.”

Yet the fishery is different, Cook said.

“The decline in fish numbers in FWP’s most upstream section, called pH shack, which is in Phase One, is more severe than could be expected due to short-term habitat loss,” he said. “I hesitate to even call it a decline, it is almost a complete loss.”

Cook said a study a few years ago suggested that very young fish from Lost Creek, Warm Springs Creek and the mainstem river itself were not surviving in the mainstem anymore.

“This almost complete lack of survival of small fish cannot be explained by habitat simplification alone,” he said. “So, what else might be going on? I think that is why there is so much alarm at what has happened to the fishery. By all indications it should not be impacted the way it is.”

The NRDP-funded study will measure current water quality and determine how it has changed since before the decline in fish populations.

Silver Bow Creek is a key tributary to the Clark Fork River. During the heyday of mining and smelting in Butte it became an industrial sewer. Superfund work in the creek began in 1999, with DEQ taking the lead, and was considered generally complete in 2015.

Monitoring at Silver Bow Creek of surface water and groundwater is ongoing, along with biological data and sediments.

The Anaconda Co. began building the Warm Springs Ponds network of settling ponds after a catastrophic flood in 1908 washed mining and smelting pollution into the Clark Fork River and all the way to Milltown.

Atlantic Richfield/BP is responsible for the ponds, which now accept the cleaner waters from Silver Bow Creek.

“The quality of the water coming out of the Warm Springs Ponds has changed over time,” Cook said.

He said Atlantic Richfield/BP has done a lot of work to optimize the ponds’ water treatment and reduce the number of water quality standard exceedances — especially for arsenic, cadmium and pH, which is a measure of relative acidity and alkalinity.

“All that said, we still have questions about how the Warm Springs Ponds warm the water and the high pH of the effluent during the summer months,” Cook said. “Nutrient impacts are also a concern.”

Nutrients can fuel algal blooms, which can rob creeks and rivers of the dissolved oxygen vital to fish and other aquatic life.

He said irrigation withdrawals along the upper Clark Fork are not a specific focus.

“But flows are a known limiting factor and there are a lot of folks working on getting more clean, cold water to the Clark Fork,” Cook said.

Meanwhile, the trout population study underway follows consultation with experts in water quality, environmental toxicology, fish biology and other areas. 

Research participants will include FWP, NRDP, USGS, EPA, university researchers and Atlantic Richfield/BP, among others.

FWP, in conjunction with Montana State University, will trap and tag fish and tackle additional research.

Cook and Uerling plan to attend a May 14 meeting in Deer Lodge of the Clark Fork River Technical Assistance Committee to discuss the trout population investigation. The public meeting will begin at 6 p.m. at the Powell County Community Center.

“There will be an update and discussion about the Clark Fork River fish population,” Cook said.