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A fly fisherman casts onto the Elk river near Fernie, B.C., Sept. 19, 2003. The Elk river is famous for cutthroat trout and is a favorite fishing destination.JEFF MCINTOSH/The Canadian Press

As it flows through the Rocky Mountains, near Fernie in southeastern British Columbia, the Elk River seems the picture of environmental health, with its crystal-clear waters supporting a world-famous sports fishery.

But a new study by U.S. researchers warns that all is not well below the surface, where invisible pollutants – including selenium, a metal-like element that can cause spinal deformities in young fish – have reached alarming levels.

"We've basically learned that the Elk River is being poisoned," Sarah Cox, interim director of the Sierra Club of B.C., said Wednesday.

Ms. Cox said a report co-authored by Richard Hauer, of the University of Montana, shows that selenium, nitrate and phosphate levels in the Elk are far higher than expected. "This study … clearly shows selenium has been collecting to toxic levels," she said. "This is a huge problem.… Definitely alarm bells are ringing."

Environment Canada had an investigative team in the Elk Valley last summer collecting water and fish egg samples, but on Wednesday the federal government wasn't able to immediately find a spokesperson to comment.

Chris Stannell, a spokesman for Teck Resources Ltd., which operates five coal mines in the Elk Valley, said he had not seen the U.S. report and couldn't respond directly to it. But he stated in an e-mail that the company "is committed to responsibly managing selenium at our operations in order to ensure the continued health of the Elk River watershed."

Mr. Stannell said the company plans to invest $600-million over the next five years on water diversion and treatment facilities and on environmental research.

The B.C. Ministry of Environment issued a statement, saying: "The concerns identified by Montana and the U.S. government reinforce the need to address the selenium issue fully – B.C. is taking the issue of selenium management very seriously on both sides of the border."

The statement also said the province will work this year with several U.S. government agencies to monitor water quality in Lake Koocanusa, a transboundary body of water into which the Elk River flows, just north of the B.C.-Montana border.

John Bergenske, of the environmental group Wildsight, said the future of the Elk River is at stake. "Clearly, we are at a very critical place … we have to make sure we reduce the levels [of pollutants] … otherwise we will lose the Elk River. I find it very, very alarming."

Dr. Hauer gathered data on the Elk River as part of a larger study that was primarily looking at the nearby Flathead River, which flows into Montana and Glacier National Park. The Flathead watershed is largely pristine, but coal mines have been proposed in the drainage, so researchers turned to the Elk River to see what might happen.

Dr. Hauer said the Elk River data is "pretty alarming," because it points to a chronic pollution problem caused directly by coal mines. "What we found was … selenium levels routinely 10-time-plus what we were observing in the Flathead. … Nitrate is 1,000 to 5,000 times higher; sulphate is a 100-fold increase," he said.

Hesaid tests upstream of mine sites on the Elk showed low levels, leaving no doubt that coal mines are the source of the pollutants. "This was quite alarming the mines would have such a significant effect," he said.

Dr. Hauer said selenium moves up through the food web, and "by the time you get up to the world-famous cutthroat trout fishery, you have selenium concentrating in body tissue."

He said when female fish collect selenium in their livers and ovaries, young fish can hatch with deformities. "High selenium levels cause spinal deformations and gills that are malformed," he said. "It causes pop eyes, so the eyes bulge out … it makes those fish unviable," he said.

The study was done by Dr. Hauer, a professor of limnology, and Erin Sexton, a research scientist, both at the University of Montana.