As permafrost thaws, some headwaters in Canada’s North turn orange and toxic: study

Ancient bedrock exposed by disappearing permafrost is releasing toxic metals into Canada’s northern rivers, a new study says, with once-pristine subarctic streams now comparable in some cases to highly acidic, contaminated mining sites.

The findings out of Yukon point to an “unfolding environmental disaster,” one co-author said, and adds to alarm over the rapid climate-fuelled changes in the North.

“We don’t know the end point, but there’s nothing about this that gives me any feeling of like, ‘oh, we’re going to be OK’,” said co-author Sean Carey, a professor at McMaster University.

“I’m not even a gloomy person. This looks pretty gloomy.”

Scientists over the past decade have documented a rise in what’s sometimes called rusting rivers. From Alaska to the Pyrenees, once-clear waters are turning a turbid bright orange in a process linked to thawing permafrost.

In some of those Alaskan headwaters, scientists documented the complete loss of two fish species and a sharp drop in biodiversity.

The paper published Thursday in a leading scientific journal gives the clearest view yet of the phenomenon in Canada’s subarctic and underlines the need to keep a closer eye on its potential impacts. The researchers looked at an area north of Dawson City straddling the Yukon and Mackenzie river basins, the largest North American subarctic rivers and major contributors to the Arctic Ocean.

The headwaters have been used by Indigenous communities and backcountry hikers for drinking water and can be critical spawning ground for fish, such as dolly varden and Arctic grayling.

“We were really shocked when we started seeing the data coming in year over year, particularly in the last two or three years, where we captured an abrupt transition,” said lead author Elliott Skierszkan, an assistant professor at Carleton University.

The study in Science used satellite imagery to pinpoint 146 visibly impacted streams. On-the-ground water quality monitoring shows some of these streams have taken an abrupt turn from pristine water to very acidic, very toxic levels of metals, especially since 2024.

“When we look at it on a broader landscape, this is happening not just in the few streams that we’ve been instrumenting, but in hundreds, possibly thousands of streams, particularly in the North American northwest,” he said.

The worst case documented by the researchers was a stream feeding the Ogilvie River. Its water quality, once pristine at the beginning of the millennium, had changed dramatically by July 2025.

The water was so acidic it would be uninhabitable for most aquatic life, with sulphur concentrations on par with a mining tailings pond. Metals, such as aluminum and cadmium, were detected at levels hundreds, if not thousands of times higher than what’s considered safe for humans and wildlife.

A plume was visible up to three kilometres downstream from where the stream met the Ogilvie River.

“We need to increase our monitoring, certainly, because there’s a mobilization of metals at toxic levels that’s happening and we need to make sure that people are aware so that they’re not at risk of consumption,” said Skierszkan.

Permafrost blanketing Canada’s North is disappearing faster than it ever has since the last ice age due to human-caused climate change driven by the burning of fossil fuels, the study says. The region, and the North broadly, is warming faster than the global average, with temperatures rising by around 2.6C since the 1960s.

Homes are being relocated and roads and airport runways are slumping as the ice-rich ground thaws and buckles in on itself or collapses into the Arctic Ocean. Methane released from decomposing soil is further heating the planet, a climate feedback loop that thaws more permafrost.

As that frozen ground thaws, ancient bedrock is also being exposed to water and oxygen.

Weathered sulphide-rich rock releases acidity and leach metals, carried by rainfall and melting snow into the streams below and degrading their water quality. It can create a visually striking barrier, with clear upstream waters suddenly turned turbid terracotta as the river meets up with a tainted stream.

“These streams look like butter chicken,” said Carey.

While the local impacts on a specific stream can be significant, the good news, for now, is that larger downstream rivers have not seen a concerning drop in water quality, Skierszkan said. While long-term sulphate levels are increasing, it’s not at toxic levels and metal concentrations are still stable, he said.

As the smaller streams feed into larger rivers, the water’s pH goes back up and the dissolved metals form into microscopic particles, giving the rivers the rusty colour.

How far downstream the water quality improves remains an open question, Skierszkan said.

Signs of trouble are not only visible in those rusty waterways but in the pockmarked hill slopes where the acid seepage originates, the study says. Water samples taken from these areas of dead vegetation were more acidic and metal concentrated than the streams below.

“These concentrations are comparable to those observed in effluents from some of the world’s most contaminated mine sites, surpassing acute toxicity thresholds for most terrestrial and aquatic organisms by several orders of magnitude,” the study says.

The comparison to a mining site is pointed in this region. In 2017, First Nations won a landmark legal case to protect the vast majority of the Peel watershed from mining and other industrial activities.

The team behind Thursday’s paper would later get funding to study the link between permafrost thaw and water quality.

Around that time, researchers in Alaska caused a stir when they reported some crystalline streams in the Kobuk Valley National Park had in the course of a year turned acidic and orange while two resident fish species, dolly varden and slimy sculpin, had disappeared.

Skierszkan, who had worked with Yukon First Nations before, reached out to the Trʼondëk Hwëchʼin government, who pointed him to headwater streams of high cultural significance along the Dempster highway corridor and Tombstone Park, he said.

For the research, Skierszkan partnered with Carey, who had been studying the area’s hydrology since the mid-1990s. Their co-authors on the paper are Matt Lindsay, a geochemist at the University of Saskatchewan, and McMaster PhD student Andras Szeitz.

“We were really able to capture the water quality initially and then this really catastrophic decline — precipitous drop in pH, metals concentrations thousands of times above water quality guidelines — all happening within a two-to-three-year period,” Skierszkan said.

The team will now shift toward trying to document the impacts of this abrupt shift, they said. Their research was awarded funding from the Canada Water Agency earlier this year to support work in partnership with Trʼondëk Hwëchʼin.

Backcountry hikers will also be encouraged to report any sightings of the rusted streams as the researchers continue trying to assess the extent of the issue.

There’s “very likely” some impacts to fish who have to move through these tainted streams, Skierszkan said. Local people depend on the fisheries for sustenance and it’s a popular tourist area, he said.

It adds another pressure on the region’s already stressed aquatic life. In 2024, Alaska and Canada put a seven-year moratorium on fishing Yukon River Chinook salmon, whose population has collapsed to less than 10 per cent of its historical average since the 1980s.

The First Nation and the territorial government did not immediately return a request for comment from The Canadian Press about the research.

This report by The Canadian Press was first published May 21, 2026.