PABLO, Mont. — In the mountain streams of southern British Columbia and northern Montana, a rugged part of the world, fish with misshapen skulls and twisted spines have been caught over the years.

Many scientists attribute the malformed creatures and declines in certain fish populations to five enormous open-pit coal mines that interrupt this wild landscape of dense forest flush with grizzly bears and wolves.

For decades, these mines owned by Teck Resources, a multinational mining company based in Canada, have been the subject of environmental concerns because of chemicals like selenium, a mining waste product, that leach into mountain rivers flowing through Indigenous land and across the border into U.S. waterways.

Selenium is a naturally occurring chemical important in the environment as a trace element. But selenium pollution has long been recognized as an extremely hazardous byproduct of coal mining. In larger concentrations, the chemical accumulates in the eggs and reproductive organs of fish and birds, and can cause a variety of detrimental effects, including lowered reproduction, deformities and death. The risk to human health from eating contaminated fish is not well understood.

Teck has repeatedly disputed various state and federal regulatory standards over what should be considered as safe levels of selenium in waterways. And those limits differ for lakes and rivers and between countries, complicating oversight efforts.

The latest case involves Montana and Idaho, where environmentalists’ lawsuits are waging a campaign over levels set by Montana for Lake Koocanusa in 2020. Its state standard is being challenged as a debate rages over cross-border pollution of the waterways, part of the war among regulators, tribal nations and scientists against Teck over whether the levels pose a hazard to aquatic life.

In a letter in the journal Science in 2020, a group of scientists warned of the cross-boundary pollution from Canadian mines and criticized what they and others attributed to a lack of regulatory oversight. “Mine assessment and permitting do not require incorporation of transparent, independent and peer-reviewed science,” they wrote. In Canada, they said, “Teck’s Elk Valley permit allows contaminant discharges up to 65 times above scientifically established protective thresholds for fish.”

They urged the Canadian and U.S. governments to begin bilateral negotiations, through the International Joint Commission, although previous appeals had gone unheeded.

In March, President Biden and Prime Minister Justin Trudeau of Canada pledged to reach an agreement by this summer to reduce and mitigate the water pollution in the Elk-Kootenay watershed. U.S. and Canadian officials say they are engaged in talks to set up a bilateral process in the coming months.

On the Montana standard, Teck has challenged the state’s levels, which are more restrictive than U.S. standards. “Significant, ongoing monitoring confirms selenium concentrations in the Koocanusa Reservoir are safe, not increasing and have been stable since 2012 and do not pose a risk to aquatic or human health,” said Chris Stannell, a spokesman for Teck.

In its annual report for 2022, the company said it was continuing “to engage with U.S. regulators to work toward the establishment of appropriate science-based standards for the reservoir.” And the company has also pointed out that there are other lakes in Montana with high levels of naturally occurring selenium.

Scientists in Montana, however, do not accept Teck’s assessments or assertions of levels in the lake, which spans the international border. Selenium levels in the Kootenai River have not decreased, environmentalists said.

At the site where the Kootenai River empties into Lake Koocanusa in Canada, levels have steadily increased well above those metrics, said Erin Sexton, a senior scientist at the Yellow Bay Biological Station, operated by the University of Montana on Flathead Lake.. “It’s a hockey-stick graph, it just goes up and up,” she said.

Provincial government officials say there are “robust monitoring and assessment programs in place” that have not detected any effects.

The environmentalists’ lawsuit is seeking to preserve the more restrictive Montana standard, which has come under fire from Republican-led lawmakers and some state agency officials. In its company report, Teck questioned whether the lower limit was in force, presumably because of the internecine feud among state authorities.

The U.S. level for selenium in rivers is 1.5 micrograms per liter in lakes and 3.1 in flowing rivers. Montana’s standard for Lake Koocanusa, after six years of research, was set at 0.8. The level for protection of aquatic life in British Columbia is 2.

Tracing the waterway chemicals

When rain falls or snow melts, waste rock from the mines leaches selenium into waterways. The level of selenium in the Fording and Elk Rivers in British Columbia near the mines have at times reached levels many times higher than provincial standards. A population of genetically pure cutthroat trout in the Fording River was decimated, at least in part, by selenium levels. In 2021, Teck was fined $60 million, a record, under Canada’s Fisheries Act for release of selenium into the Fording River.

The Elk River flows 140 miles from its source until it enters Lake Koocanusa, created by the damming of the Kootenai River, which straddles the border. The lake becomes the Kootenai River again below the Libby Dam in Montana and Idaho, and it flows back north into Kootenai Lake in British Columbia. Eventually it empties into the Columbia River.

Unlike in an oil spill, the effects of high selenium levels do not result in large kills of fish that suddenly appear belly up in the water. Instead, selenium poisoning reduces fish numbers by causing mortality in the larval stage.

“It’s a really nasty contaminant because it causes deformities in reproductive organs,” Ms. Sexton said. “They call it an invisible contaminant because they fail to thrive. You don’t find eggs that don’t hatch.”

Indigenous land concerns

U.S. and tribal officials argue that the mining-related presence of chemical pollution violates the 1909 International Boundary Waters Treaty. Tribal leaders in the United States claim it may breach their treaty rights of 1855, which guarantee “taking fish at all usual and accustomed places.” They want the International Joint Commission, a U.S.-Canadian body that oversees trans-boundary disputes, to study the issue and prepare recommendations for cleanup.

But the government of British Columbia has continued to oppose efforts to remedy the situation, Montana officials say.

Part of the problem, Ms. Sexton said, is that the province of British Columbia allows industries, including mining companies, to largely monitor themselves and offer evidence produced by their own scientists.

Mr. Stannell pointed out that the company had spent $1.2 billion on wastewater treatment near the mines, and planned to spend $750 million more to improve water quality in the coming years.

A region rich in coal

Coal mining in this Canadian province began more than a century ago, though the methods changed in the 1980s, when underground mining was largely abandoned for open pits.

High-grade metallurgical coal is mined using a method called cross-valley fill, similar to the mountaintop-removal technique employed in West Virginia and some other states. Explosive charges blast away the top of the mountains, removing whole sections of a range, to expose rich deposits of coal. Giant shovels and massive 550-ton dump trucks mine the coal, which is transported by rail to Vancouver and then by ship to Asia, where it is essential for steel manufacturing.

Other mining-related pollutants, partly from the extensive use of explosives in the blasting, include cadmium, sulfates and nitrates, experts say.

Teck’s open-pit mines produce more than 21 million metric tons of coal a year. An analysis issued last year by the British Columbia Chamber of Commerce estimated that the company provided nearly 13,000 jobs in the province and $4.6 billion to its gross national product.

The company is seeking to expand one of its five Elk Valley mines, and it has applied to open two new ones.

Calvin Sandborn, the legal director of the Environmental Law Center at the University of Victoria and one of the authors of a 2021 report, accused the governments of British Columbia and Canada of deliberately failing to regulate Teck.

“If they had acted on the warnings of their scientists years ago, they would have dealt with this problem,” Mr. Sandborn said. “And they didn’t because it’s a corporation that’s too big to fail.”

According to the Elk Valley Water Quality Plan, British Columbia allows Teck to continue to operate its mines as long as it stabilizes selenium levels and eventually reduces them after 2030.

Scientists worry that the existing mines could pollute the rivers for centuries. And some do not believe the technology exists to remove enough selenium from flowing rivers or groundwater to reach safe levels. Ms. Sexton said Teck could do more to seal the contaminants in the waste rock.

Critics of government policies point out that when John Horgan stepped down from his post as premier of British Columbia in 2022, he became a member of the board of Elk Valley Resources, a spinoff of Teck Coal, created to manage the mining resources. According to BIV, a publication that covers business in British Columbia, board members are paid at least $235,000 annually.

The Canadian Ministry of the Environment and Climate Change Strategy did not respond directly to questions seeking a response to accusations that the government’s oversight of the mining giant was inadequate or lax.

“We are pleased that Canada and the United States have committed to working together to reduce and mitigate the impacts of water quality concerns,” said David Karn, a spokesman for the agency. “Protecting and enhancing water quality is a key priority, and through our regulatory activities, we continue to undertake and oversee projects to improve and protect water quality in the Elk River Valley and Koocanusa Reservoir.”

New policies cannot come soon enough for Indigenous people and conservationists in both countries.

The mining on the ancestral lands of the Kootenai people, (known as Ktunaxa in British Columbia), has become a longstanding issue. “Over a century of mountaintop-removal mining has laid waste to the traditional territory of the Ktunaxa Nation, contaminating the Kootenay River and fish that depend on it,” the six governments of the tribal nation said.

“Our native fishery is extremely important to us,” said Tom McDonald, chairman of the Confederated Salish and Kootenai Tribes at their headquarters in Montana and a fisheries biologist. “Water to us is almost considered holy water. It’s very sacred.”

“You catch a fish and its gill plate is missing or its jaw is all malformed, are you going to eat it?” Mr. McDonald said. “No, you are not going to. When you lose that ability to fish, it disconnects you from your culture. It takes a whole thing away from the people — their society, their sense of place, their community and their family. It’s an extreme taking.”

The Kootenai/Ktunaxa tribes have worked to protect water quality and fisheries in their territory. The Kootenai band in Bonners Ferry, Idaho, has a long-term program to restore burbot to the Kootenai River. The long, eel-like fish, known for its flaky white flesh, is important for subsistence fishing, and it almost became extinct before the tribe built a hatchery to rear fish for introduction back into the river. Now, selenium has been found in the fish there.

Whitefish populations below Libby Dam, which created Lake Koocanusa, have declined considerably in recent years. Monitoring in 2018 found that populations, which are usually 700 fish per 1,000 feet, were down 53 percent in 2018 and 55 percent in 2023. High levels of selenium, above state and U.S. limits, have been found in fish eggs and ovaries.

The selenium from the mines “is likely causing the decline,” said Jim Dunnigan, a fisheries biologist for the Montana Department of Fish, Wildlife and Parks who is studying the contamination. “It’s cause for serious concern.”

Wyatt Petryshen of Wildsight, the Canadian environmental group that monitors Teck’s operations, said environmentalists were worried about recent moves by Teck that split its operations into Teck Metals Corp. and Elk Valley Resources, which will own the coal-mining operation.

“There are very real concerns that Teck is trying to spin off the company to avoid paying for environmental damages while maintaining cash flow to their metal mining business,” Mr. Petryshen said.

Sheila Murray, chairwoman of Teck’s board, defended the change, saying it would be more profitable for shareholders and would “support a sustainable future for the benefit of employees, local communities and Indigenous peoples.”

U.S. officials and advocates said the International Joint Commission, the bilateral body, would be the best authority to seek ways to contain and reduce the mining pollutants. “We need a scientific advisory panel of both U.S. and Canadian scientists,” Mr. Sandborn said. “We need to get this to the International Joint Commission so that we have a proper watchdog.”

Jennifer Savage, a spokeswoman for the U.S. State Department, which oversees the United States’ role in the commission, said it wanted the international body to take the matter up soon.

“Indigenous communities along the watershed depend on these waters for cultural survival and for their survival,” said Ms. Savage, director of the department’s office of Canadian affairs. “We’re impatient. We are definitely eager to find a solution.”