The Yellowstone river has its headwaters in the mountain streams and snowy peaks of the famous US national park with the same name, and makes an unfettered downhill run all the way to the Missouri river, nearly 700 miles away. It is the longest undammed river in the Lower 48 states.

Last August, the Yellowstone made national headlines when a parasite killed thousands of fish, mostly whitefish. Fear of spreading the parasite to other waterways forced Montana officials to close the river to fishermen, rafters, and boaters. At the height of summer, the stunningly scenic, trout-rich river was eerily deserted. Fishing re-opened in the fall, but the parasite has been found in other Montana waterways.

That a non-native parasite somehow got into a river may seem like an unremarkable occurrence. But a new, expansive model of gravel-bed river systems in mountainous areas, such as the Yellowstone, depicts a more complex scenario in which a host of human activities combine to degrade river systems and render them more vulnerable to destructive outside influences such as parasites. This body of research – 40 years in the making, but much of it summed up in a recent paper – rewrites the understanding of the ecological dynamics of these rivers. And it casts a harsh light on human river valley activities such as homebuilding, dam construction, irrigation, and channelization that may be slowly choking highly dynamic river systems – and the biodiversity that depends on them – to death.

The waters of the Yellowstone, for example, have been diverted for irrigation, and the course of the river has been altered by channelization for flood control and the placement of boulder breakwaters, or riprap, which landowners install to stem erosion. Although the Yellowstone is undammed, these other human activities can slow and change the river’s flow and, most significantly, alter the complex interaction between the above-ground course of the river and the unseen currents that stream beneath the Yellowstone Valley’s broad gravel and cobble bottom. Such human alterations to a river can impair its dynamism and resilience, especially in combination with rising temperatures from climate change and reduced water flows because of increased evaporation and irrigation.

In effect, these myriad human activities contribute to the weakening of the “immune systems” of rivers like the Yellowstone, making aquatic organisms more vulnerable to stresses like fish-killing parasites. The paper said these pernicious changes are being experienced in waterways across western North America and in other mountain river systems, including some found in Europe, the Andes, the Himalayas, and the high country of New Zealand.

Most of the world’s gravel-bed rivers have experienced degradation, and in many places managers are trying to walk back the damage. On the Snake river near Jackson, Wyoming, for example, local and federal officials are working to restore riparian habitat damaged by the construction of 22 miles of 15-foot-high flood-control levees in the mid-20th century. The levees enabled some construction to take place in the floodplain, but deprived the river of its ability to flood and carry out other ecological functions.

In Europe, most mountain rivers have been tamed dramatically over the past several centuries. The Drava river – which flows out of the Alps through Croatia and Austria and into the Danube – has been constrained historically by farming, hydroelectric dams, and flood control. In recent years, however, conservationists and government officials have launched major restoration programs to reconnect tributaries and floodplains and to restore riparian areas of the Drava.

The life that depends on healthy, mountain river systems is legion. The recent paper, published in the journal Science Advances, brought together an array of researchers from different disciplines, from bear biologists, to ornithologists, to ungulate biologists. They were surprised to find the large number of species that rely heavily on the biodiversity generated by the Yellowstone ecosystem, not just fish and other aquatic species.

Although river floodplains themselves make up only roughly 3% of many river valleys, “these gravel-bed river systems are where the magic happens,” said Richard Hauer, a professor of limnology at the University of Montana and lead author of the paper. “Two-thirds of species spend part of their lives in the floodplain.”

Some 70% of bird species in mountain river valleys, for example, rely on habitat created by the river system.

In the new model set forth in the Science Advances paper, melting snow and groundwater flow down the channel of the river, but the vast majority of the water in the system is moving far more slowly through the labyrinthine underground networks of cobbles, gravel, and sand that make up the entire valley bottom, from the base of one mountain range to the other.

This subterranean habitat is far more biologically productive than previously thought and is home to microbes and aquatic insects, such as stoneflies, which are critical to a river’s food chain. Water is constantly flowing through the matrix of rock and sand, which filters out organic material and releases nitrogen, phosphorous, and other nutrients that well up through the entire system. These nutrients then are made available to plants and insects on the surface – a jolt of biological adrenaline.

This nutrient pulse is the foundation of a food chain that creates biodiversity in the entire valley, nourishing willows, cottonwood, and aspen, which in turn draw birds and beavers, elk and caribou. Wolves and grizzly bears then are drawn to the prey.

This is a far more expansive and detailed picture of river ecosystems than previous models. Until this work began in the 1970s, researchers thought the hyporheic zone – the groundwater that is part of the river system – lay within just a meter or so of the river bottom and banks. Now it’s clear it takes up most of the river valley.

“I’ll never look at a river the same way again,” said Michael Proctor, an independent grizzly bear biologist in British Columbia who is one of the paper’s authors. “It gives my argument to protect river valleys for grizzlies a powerful punch, because I am not just arguing for bears, but for a wide diversity of nature.”

These river systems play other roles. The above-ground river continually jumps channels and makes networks of new ones. Abandoned channels, meanwhile, become covered with gravel and are transformed into important habitat for stoneflies and other insects that feed fish. Water flowing through the gravel beneath the valley floor surfaces in a myriad of places along the floodplain, creating a constantly changing assortment of ponds, seeps, springs, and other important habitat.

Interaction between water in the river and groundwater is fundamental to the river ecosystem. During the winter, cold water is stored in the rock and gravel, surfacing in the summer to moderate warm temperatures. Pools of warmer water in winter and cool water in summer create refuges for fish and other species.

This mix of water plays a role in preventing disease, which is part of the story of the incursion of parasites into the Yellowstone. As water is withdrawn for irrigation and structures such as riprap are installed, the mixing between groundwater and river water is reduced. That means less cold water is stored in the gravel to cool the river in summer and warm the river in winter.

“There’s a whole suite of really bad things that happen from this hardening that directly affects the fishery,” says Hauer. “[Fish] pool in warmer water and are stressed.” Their metabolism increases in warmer water, “and they are not able to eat enough food and they are not healthy. That makes them really vulnerable to disease.” Crowding in the cool water that remains may bring them into contact with more parasites, while warmer water may favor increased populations of parasites.

Meanwhile, invasive zebra and quagga mussels – a growing problem in the western US that upsets the ecology of freshwater ecosystems – also favor warmer water. The degradation of river ecosystems may help them thrive, research shows.

These harmful effects – coupled with reduced water flows from climate change, longer summers, and warmer water and air temperatures – are greatly diminishing the resilience of gravel-bed rivers, Hauer says.

Dead whitefish float in the Yellowstone river in August 2016. Photograph: Matthew Brown/AP

Another important feature of a free-flowing, gravel-bed river is their unruliness. They are physically disruptive, constantly churning, tearing riparian habitat apart, rebuilding and renewing the system, especially during high water. Rivers wash topsoil, gravel, and woody debris from one spot to a new home downriver, which creates an array of new ecosystems. That, in turn, restarts plant succession. This blends with existing habitat – everything from mature cottonwood forests to grasslands – to fashion a complex patchy mosaic that increases biological richness.

“If you take the power out of the river with a dam or riprap,” says Hauer, “there’s no renewal – the river doesn’t move gravel around and doesn’t create new mosaics of habitat. Nutrients are not dispersed. Everything gets locked in place and starts getting old and declines.”

The implications of this new model for conservation are enormous – and could make the conservation of rivers more difficult since it implicates human activity on a much broader scale. Scientists say that if we continue to take bits and pieces out of these ecosystems, rivers such as the Yellowstone will continue to decline, especially as the effects of climate change mount.

“People don’t like to hear that what they are doing is killing the river,” Hauer said. But he maintains that society needs to know how its activities are altering the natural world if it hopes to fix ecological problems. “The first thing an alcoholic has to do is stand up and say ‘Hi my name is Ric and I’m an alcoholic,’” said Hauer.