“Eventually, all things merge into one, and a river runs through it.” Norman Maclean penned these famous words about Montana’s Blackfoot River, a tributary of the Clark Fork and one of the most celebrated trout streams in the American West.
Montana’s largest river by volume, the Clark Fork stretches 310 miles from the Continental Divide near Butte and Anaconda, threading through wide agricultural valleys and tight forested gorges, swallowing the Blackfoot, the Bitterroot, and Rock Creek before finally meeting the Flathead and pushing west toward the Columbia. Its watershed covers more than 22,000 square miles and drains some of the most storied trout water in the country. At its heart, the Clark Fork flows through the middle of Missoula, where you can dine at a riverfront restaurant and witness a 20-inch rainbow rise in the evening light.
But this wasn’t always the case. The Clark Fork and its tributaries faced poor watershed management, industrial mining, and a string of other conservation issues. Today, beneath the surface runs another current, the legacy of decades spent trying to reverse a century of damage to this fabled watershed.
A Superfund Story
In the late 1800s and early 1900s, Butte was a copper boomtown. Mining and smelting operations generated vast quantities of tailings laden with lead, arsenic, cadmium, and zinc, much of which accumulated throughout the upper Clark Fork basin. The river carried the consequences for decades.
In 1908, a late-season snowfall of nearly 2 feet across the basin turned to rain and triggered a catastrophic flood. The resulting floodwaters moved tailings from Butte and Anaconda across 120 miles of floodplain, in some places extending 5 miles on either side of the river. Much of the contamination settled at the bottom of the Milltown Reservoir, just above Missoula at the confluence of the Blackfoot and Clark Fork rivers. Developers erected a hydropower dam in 1905, turning the still water behind it into a toxic archive. “Silver Bow Creek, the headwater stream of the Clark Fork, was roughly a sewer during the mining boom,” says Brian Chaffin, executive director of the Clark Fork Coalition (CFC).
By 1981, Bonner and Milltown residents developed arsenic poisoning, traced to contaminated drinking wells. Arsenic migrated from the reservoir sediments into the municipal water supply. Congress passed the Superfund law in 1980, holding companies retroactively liable for industrial contamination and compelling cleanup, and the Milltown site was eligible. For years, the proposed remedy was to fence off the reservoir, leave the contamination in place, and pipe in clean drinking water indefinitely. However, the CFC, Trout Unlimited (TU), and community advocates fought back through years of litigation and congressional pressure.
In 2003, the Environmental Protection Agency issued a new decision to remove the dam, excavate the contaminated sediment beneath the reservoir, and restore the river, completing one of the largest river restoration projects in U.S. history. Dam removal wrapped up around 2011, and the floodplain was remeandered. Cottonwood and willow returned naturally after a post-remediation flood validated the restoration design. “Rivers need room to move,” Chaffin says. “Dams and channelization force a river into an unnatural configuration that doesn’t allow it to function seasonally or over time.”
John Herzer, owner of Blackfoot River Outfitters in Missoula, has guided locally for over 35 years. “Within literally weeks of the dam coming out, we caught lower Clark Fork rainbows, big 16- to 19-inch fish that typically lived below town, in the upper Clark Fork above Rock Creek,” he says.
Cold Water, Wild Fish
The Middle Clark Fork runs roughly 105 miles between the Blackfoot confluence and the Flathead River, known to the Salish, Indigenous people of western Montana, as “the Place of the Big Bull Trout.” The watershed remains one of Montana’s most important strongholds for bull trout, a threatened cold-water native species that has disappeared from much of its historic range across the West. Today, the river supports six trout species, including native bull trout and Westslope cutthroat alongside brown, rainbow, cutbow hybrids, and brook trout, plus whitefish, northern pike, and smallmouth bass.
To understand the Clark Fork, think of it as three distinct rivers. “The upper river, toward Butte, is tight and small, like a meadow stream with undercut banks and overhanging willows. By the time it hits Rock Creek, about 10 or 12 miles outside Missoula, it’s quite a bit bigger,” Herzer says. “Below Missoula, after it collects the Blackfoot and the Bitterroot, it becomes a different river; wide, slow, and meandering. Then you reach the Alberton Gorge, about 30 miles below town, where Class 3 whitewater cuts through cliffs and boulders above pools 30 feet deep.”
In the section that flows through Missoula proper, the fishing is remarkable. One of the most popular holes in the area sits right behind the DoubleTree Hotel, where Rattlesnake Creek, a spring-fed tributary, enters the Clark Fork and creates a thermal refuge. Rainbows, browns, and cutthroats hold along a cold-water seam, and on any given evening, you’ll find an angler casting into the confluence as trout sip insects in the fading light. “The average fish we catch below Missoula probably exceeds 16 inches, a lot of 18s,” Herzer says. “But 20-inch fish aren’t uncommon.”
The Clark Fork’s wild fish owe their resilience to a late-1960s policy shift: the Wild Trout Management Program, born when biologist Dick Vincent discovered hatchery trout were suppressing wild populations on the Madison River. By 1974, Montana’s Fish and Game Commission phased out statewide stocking, helping build the blue-ribbon wild trout fisheries Montana is known for today.
The River’s Keepers
The Clark Fork Coalition was formed in 1985, three years after the Milltown arsenic poisoning came to light, and four years after the Superfund law gave conservationists a legal lever. Today, the organization works in three lanes: on-the-ground physical restoration, science-based water policy advocacy, and community engagement. It employs 13 full-time and 5 seasonal employees. Unusual for a watershed nonprofit, the CFC owns water rights.
“In Montana, water rights follow the doctrine of prior appropriation, first in time, first in right,” Chaffin explains. “Montana didn’t recognize instream flow, meaning water held in a river for fish and wildlife, until about 1970. We acquire water rights, historically used for agriculture, irrigation, or other purposes, and convert them to instream flow through a state process.”
The CFC also owns senior water rights, a fact that became legally significant in 2016 when the organization challenged a loophole in Montana’s 1973 Water Use Act. The Act required permits for new water rights but carved out an exemption for small groundwater uses, such as a domestic well on a rural property or a stock tank. As Montana’s population grew, notably after the 1992 film adaptation of A River Runs Through It sparked a cultural pilgrimage that hasn’t slowed, developers exploited the exemption to drill wells for sprawling subdivisions without permits. In CFC v. Tubbs, the Montana Supreme Court ruled that regulators must consider the cumulative impacts of exempt wells when evaluating development near waterways.
The CFC remains vigilant against efforts to weaken water protections, working alongside ranchers, municipalities, and conservation groups to safeguard the watershed. TU worked with federal partners to secure a Good Samaritan authorization that allows nonprofits to clean up abandoned mines on public lands without assuming liability. “It’s a huge win for water quality,” says Paul Parson, TU Montana restoration director. “Abandoned mines are one of the biggest issues we face here.”
What Hangs in the Balance
While Montana still has more cows than people, the state has added more than 60,000 residents since 2020, according to the U.S. Census Bureau. “People watch Yellowstone and dream of freedom, space, and clean water,” says Andrew Gorder, CFC policy and legal director. “That means more competition for limited water supplies.”
Across western Montana, growth takes the form of sprawling ranchette subdivisions carved from agricultural land. These developments rely on private wells drawing from shared aquifers and individual septic systems rather than municipal infrastructure. The result is a double strain on the watershed: reduced streamflows and nutrient pollution that can eventually seep into nearby waterways.
“We’re seeing climate change in real time,” Gorder says. Snowpack is shrinking, spring runoff arrives earlier, and rivers that once stayed high through summer now surge for a few weeks before crashing. The result is warmer water, lower late-season flows, and more algae blooms. “All of it was predicted. Now it’s playing out on the landscape.”
For bull trout and Westslope cutthroat, the Clark Fork’s two native trout species, the math is unsparing. Both depend on cold, clean water, and as temperatures rise and flows decline, they lose ground. “We’re already seeing warmer water creep further up the basin,” Gorder says. “Species like northern pike and smallmouth bass are establishing themselves in stretches that were once exclusively cold-water fisheries.”
Herzer recalls when hoot owl restrictions weren’t necessary on the Clark Fork. Named for the hour when owls hunt, hoot owl restrictions prohibit fishing on designated waterways between 2 p.m. and midnight during the hottest summer months. Trout, which thrive in water between 50 and 65 degrees, experience serious physiological stress above 70 degrees. At 73 degrees, sustained for three or more consecutive days, Montana Fish, Wildlife & Parks (FWP) can pull the trigger on closures. A trout caught and released under these conditions is unlikely to recover.
“For the first 15 years I guided here, it was never an issue,” Herzer says. “Even the lower Clark Fork stayed cool because there was so much water. Now it gets down to 1,200 CFS in late summer. It used to run at 4,000. Each year, the restrictions start earlier.”
Restrictions vary across the state and can shift quickly as conditions evolve throughout the summer. Anglers planning a July or August trip to the Clark Fork basin should check Montana FWP’s Current Waterbody Restrictions map.
This summer, two development proposals at opposite ends of the watershed alarm anglers and conservationists alike. In the Blackfoot headwaters, the Montana Department of Environmental Quality approved an Australian mining company, Sentinel Metals, to drill up to 21 exploratory wells at its Columbia Gold Project near Lincoln. Officials concluded the drilling itself would cause only minor, temporary impacts and didn’t approve an actual mine. Meanwhile, on the river’s lower stretch in Bonner, plans for an AI data center fell apart in early July after the property owner pulled his support amid concerns over water use and the shared aquifer. Missoula County is now moving to temporarily ban new data center projects, according to the Missoula Current.
Conservationists point to history as a cautionary tale for the mine’s path forward. In 1975, a tailings dam failure on Mike Horse Creek, a Blackfoot headwater tributary, sent mine waste downstream and devastated the fishery, echoing the contamination that spread across the Clark Fork basin during the catastrophic 1908 flood. It took decades and hundreds of millions of dollars to rebuild the fishery.
The Next Current
More anglers fish the Clark Fork now than ever before. The CFC’s River Ambassadors Program, a collaborative initiative with the city of Missoula, Missoula County, the Conservation District, the University of Montana, and FWP, stations seasonal staff at put-ins and takeouts on the Clark Fork, Blackfoot, and Bitterroot to educate and assist river users. Float counts have nearly doubled since 2018, from roughly 20,000 to 36,000 people on the water during the summer months, according to the CFC.
More people on the river means more advocates. “People complain about boat traffic,” Herzer says. “But those boats are full of people who will fight to protect the river when its water quality is threatened. That’s a good thing.”
Few newcomers fathom what it took to get here. “People arrive in Missoula and assume the river has always been this pristine and full of trout,” Chaffin says. “They don’t see the decades of work it took to get here, or the work that’s still required to sustain it.”
Conservation is never finished. Cleanup continues across the upper basin, while warming water, invasive species, and growing development pressure test the river’s recovery.
“Two hundred years ago, entire Salish nations lived off bull trout in this fishery,” Parson says. “The river is getting better, but it’s nowhere near what it was a century ago.”
It’s one of the West’s great conservation success stories. Yet no one who knows the river mistakes success for an ending.
Just above Missoula, the Blackfoot joins the Clark Fork, merging water that has ferried Native communities, miners, loggers, anglers, and conservationists through vastly different eras. What comes next depends on the same thing that brought it this far: people willing to do the often-invisible work of protecting what they love.
“Everything comes back to water,” Herzer says. “If you have water, the river takes care of itself. The trout take care of themselves.”
Maclean wrote that eventually all things merge into one. On the Clark Fork, past and future still run in the same current, one generation’s work carried downstream to the next.
