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MISSOULA, Mont. — They are beautiful, glistening icons of the West, filled with life and history. But there is far more to mountain rivers, scientists are learning, than the water churning between their banks.

In a paper published earlier this year, a team of ecologists sought to outline the essential role of gravel-bed rivers in Western mountain ecosystems — the first time an interdisciplinary team has looked at river systems on such a large scale.

Grizzlies cross the Red Deer River in Alberta, Canada Credit Peter Mather

Grizzlies cross the Red Deer River in Alberta, Canada Credit Peter Mather

“A river doesn’t just flow down the channel,” said F. Richard Hauer, a professor of stream ecology at the University of Montana and the lead author of the paper. “It flows over and through the entire flood plain system, from valley wall to valley wall, and supports an extraordinary diversity of life.”

Perhaps most surprising of all: “Most of the water in these systems is not in the river — it’s in the gravel.”

These river systems are among the most ecologically important habitats on the continent, Dr. Hauer and his colleagues concluded, supporting a hidden wealth of biodiversity. And not just in the West; the life-sustaining dynamics are at play in the mountains of Europe, the Andes, the Himalayas and New Zealand.

In the West, a dynamic river is not important just to fish or to amphibians, but to grizzly bears and mountain lions descending from mountaintops to the flood plain for important foods. Indeed, two-thirds of the species in a large river valley spend at least part of their lives in its flood plain.

Trout in Ole Creek, a tributary of the Flathead River in northwestern Montana.

Trout in Ole Creek, a tributary of the Flathead River in northwestern Montana. Credit Johnny Armstrong

The new study also demonstrates that altering this complex biological machinery with dams and diversions has far-reaching effects, leading to long-term decline of the ecosystem.

“A river is a huge, huge biodiversity engine with multiple parts,” Dr. Hauer said. “If you keep taking out parts, pretty soon the engine stops.”

Until now, scientists had never put together such a comprehensive ecological blueprint of river dynamics.

Melting snow and groundwater flow down the channel; this is what we think of as a “river.” But underground, far more water is moving slowly through a labyrinthine network of cobbles, gravel and sand that make up the entire valley bottom.

This deeply buried habitat is far more important and far more productive than thought. The matrix of gravel and sand cleans the water, filtering organic material and freeing up nitrogen and phosphorous embedded in the gravel.

These natural fertilizers spread across the valley bottom, a shot of adrenaline that nourishes plants in the flood plain such as willows and aspen, which in turn draw birds and beavers, elk and caribou. The plant-eaters attract predators like wolves and grizzly bears.

In the summer, warm water is stored underground. It takes so long for the water to move that it surfaces in winter, moderating water temperatures and creating a refuge for some aquatic species, shielding them from winter’s freeze. In the winter, the opposite happens.

The river also continually rearranges and renews the ecosystem.

During high water, topsoil, gravel and woody debris are washed into new sites downriver and below ground, fostering new habitats and new plant communities. The new habitats blend with existing ones, from mature cottonwood forests to grasslands, to create a patchy mosaic.

On a recent flight over the Bitterroot River, a gravel-bed river near Missoula, Dr. Hauer pointed out the flood plain.

While the river below flowed down a main channel, it was easy to see from the air that over centuries, the Bitterroot had frequently jumped its bounds to create a network of new channels.

The old channels were covered with gravel — an important habitat for the stoneflies and other insects that feed the fish. Everywhere in the valley, water flowing underground through the gravel surfaced to create a diverse assortment of ponds, seeps and springs.

Dr. Hauer also pointed out a number of places where people have sought to tame the river’s unruly habits in order to plow farm fields or build subdivisions.

“There’s no renewal — the river doesn’t move gravel around and doesn’t create new mosaics of habitat,” he said. “Nutrients are not dispersed. Everything gets locked in place and starts getting old and declines.”

The environmental damage is hidden — at first. Channels feeding the underground habitats are sealed off as the river is confined. The species that depend on the hidden flows begin to falter.

These gravel flood plains, Dr. Hauer said, are among the most endangered ecosystems worldwide.

Keeping them intact will help dependent species adapt to the greatest environmental threat of all: climate change. “The implication for conservation is enormous,” Dr. Hauer said.

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