WISE River, Mont. — Since the Fellin family founded the Big Hole Lodge in the 1980s to take people fly fishing on the Big Hole River, they have seen significant changes to the cobble-and-boulder-studded freestone trout stream.

For as long as anyone can remember, this river originating high in the Beaverhead mountain range had always been clogged with ice and deep snow every winter, preventing the start of fishing season until June. Now the river is ice-free by April or May, and the Fellins open the lodge earlier to welcome anglers eager to cast a fly.

The signs of an altered river ecosystem are hard to miss. Clouds of insects no longer hover in such big swarms, and some key species, like the salmonfly, that are critical sources of food for fish are less abundant.

Those shifts are occurring at the same time that state biologists report that the numbers of brown and rainbow trout in the river have plummeted over the last seven years to historic lows, with strange maladies afflicting some of the most sought-after fish.

In addition to their diminishing ranks, “we’ve seen whirling disease, red sores and lesions on fish, and brown trout with cauliflower fungus,” Wade Fellin said over coffee in the dining room of the rustic lodge that serves the business started by his father, Craig, in 1984.

“The brown trout are blind, and still alive,” he added, joining others in calling them zombie trout.

The rainbow and brown species are the quarry for many who fish, introduced to the region in the 19th century. Twenty years ago, fishery biologists were counting about 3,000 fish per mile along the Big Hole River. That number has dropped precipitously to hundreds in some stretches.

In May, the number of trout per mile fell so low in some sections that the Fellins, other guides and outfitters and business owners formed a nonprofit organization called Save Wild Trout and urged Gov. Greg Gianforte to create a task force in the hope of stemming the deepening losses.

“We have an emergency in southwest Montana’s rivers, and we need to act immediately to avoid a total collapse of those trout fisheries,” they wrote. “This is an all-hands-on-deck moment.”

For businesses and enthusiasts alike, the 155-mile Big Hole River is not the only cherished waterway in the state to be eliciting such concerns. Other rivers in the Jefferson Basin — including sections of the Beaverhead and the Ruby, both top trout streams — have experienced similar declines, as has the upper Clark Fork, though some experts suggest the latter that may be partly related to runoff from past mining.

Unlike many states, Montana does not stock its rivers with hatchery-reared fish, depending instead on wild populations to sustain themselves. If the trout population crashes here, it might be a long time before it recovers.

Environmental groups have also recently sued to have the Arctic grayling, a distinctive-looking native fish, listed as endangered because of its dwindling numbers. The Big Hole is the only river in the lower 48 states where it’s found.

All of that adds uncertainty to the future of fly fishing for Montana, where catching trout with artificial insects gently lofted onto the surface of cold flowing water is not just a pastime but part of the state’s identity.

Despite the worrying conditions, the Big Hole still bustled recently with anglers in rafts and drift boats. With summer winding down, the streams are cooling, and that may grant the fish a reprieve.

One of Craig Fellin’s first clients was the writer Thomas McGuane, whose book “The Longest Silence” captured his experience:

“I was swept away by the perfection of things, by the glorious shape of each trout, by the angelic miniature perfection of mayflies, and by the pure wild silk of the Big Hole River. It is for such things that we were placed on this careening mudball.”

It’s been roughly 30 years since interest in fly fishing soared upon the release of “A River Runs Through It,” the Robert Redford film based on the book by Norman Maclean, and it surged again during the pandemic as people sought outdoor activities. Important to Montana’s economy, angling tourism contributes an estimated $900 million a year to the state’s revenues.

The Big Hole has long been subject to warm temperatures and low flows in the summer. In 1995, Craig Fellin was one of the founders of the Big Hole Watershed Committee, a group of valley residents formed to find voluntary ways to ease pressure from irrigation and fishing.

But lately things have grown worse, with tensions rising among the competing forces of fishing enthusiasts, the businesses that cater to them and the state’s residents. Some blame the outfitting industry, targeting the companies’ vehicles and drilling holes in their gas tanks.

The younger Mr. Fellin, who studied water law and is the manager of the lodge and a guide, said the state’s fly fishing industry would have to shoulder some of the responsibility of helping fish survive.

The sport has exploded along the state’s rivers, with many fearing that trout are being “loved to death.” For example, the number of angler days — which is any part of a day spent fishing per person on any given day — on the Big Hole increased to more than 118,000 in 2020, up from 71,553 in 2011.

The situation has become so pressing that the state has imposed a number of restrictions, including an unusually high number of river closures and “hoot owl” limits — which end fishing in the afternoon when the water warms. And to protect spawning brown trout, Montana officials have decided to halt fishing two weeks earlier than usual, on Sept. 30, for portions of the Big Hole, Ruby and Beaverhead Rivers.

Last month, Governor Gianforte visited the Big Hole valley, appearing in Wise River before a house packed with those affected by the fishing concerns. He did not, as the group had hoped, say he would appoint a task force, but instead delegated the work to state fishery experts. The Save Wild Trout organization has contracted with its own scientist to assess water quality and study possible causes of the steep declines. The research will take place over the next several years.

Experts believe that a combination of factors has caused the collapse. At the top of their list of suspects is the climate: Montana has warmed 2.7 degrees Fahrenheit since 1950, and the pace is quickening, especially in the winter and spring. Those seasons are critical for replenishing the rivers with the cold, clear water that trout thrive in. Temperatures in the high mountain valleys of the Rockies are increasing twice as fast or more than temperatures nationally.

“There is an ongoing aridification of the West,” said Steven W. Running, a professor emeritus of ecosystem and conservation sciences at the University of Montana. “As it warms up, evaporation increases and precipitation is not increasing, the snow melts earlier,” he said. “Once you’ve melted through that snowpack, there is nothing to cool that water down” as it flows into the rivers.

“We’re not getting the high flows that flush the sediment out of the river” and help maintain a healthy fish habitat, added Brian Wheeler, executive director of the Big Hole River Foundation, a nonprofit organization in Dillon, Mont., that monitors water quality.

Mr. Running noted that warmer water has lower levels of dissolved oxygen for the fish, “and that is what really pounds them.”

State officials agree that climate plays a major role. “Fish are continually getting stressed through the summer with the drought conditions and going into another stressful situation in the fall when they are spawning,” said Eileen Ryce, head of the fisheries bureau for the Montana Department of Fish, Wildlife and Parks. “All of that is hard on fish survival. On top of that, you add angling and handling of fish.”

Many trout are caught and released, but anglers’ handling of them can remove a layer of protective slime, and playing a hooked fish at the end of the line can weaken them.

Fish can then become susceptible to pathogens. A common fungus appearing on the fish is saprolegnia, Dr. Ryce said, but it is emerging with alarming frequency.

Researchers have not determined the cause of the lesions, and no novel pathogens have been found, she said. The state has opened a web portal where people can submit descriptions or photos of ailing trout.

Other likely contributors to the trout’s disappearance include competition for resources from agricultural practices, some say. Ranchers along the river divert water from the river to their fields to grow alfalfa for hay. While the irrigation method is legal, it drastically reduces flows in summer months and exacerbates harm to fish.

Manure from cattle grazing on fields along the river leaches nutrients into the stream causing algae blooms. “They flood-irrigate those fields, and so we are making tea out of the manure,” Mr. Fellin said. If poorly managed, cattle trample and degrade stream banks.

Some ranchers though have made changes to assure the health of the Big Hole, which is situated in a county that has more cattle than any other in the state. “We work diligently to fence riparian areas off,” said JM Peck, who owns and manages the Trapper Creek ranch, near Melrose, with others in his family. “And we work very hard to give water back when times are tough. It’s a shared sacrifice.”

Insect population research is also underway, with one focus on salmonflies.

Jackson Birrell, director of the Salmonfly Project, which studies the decline of aquatic insects throughout the West, warned that the so-called insect apocalypse was real and said that if it continued, it could substantially affect trout populations. One study on a Colorado river found that salmonflies accounted for slightly more than half of the trout diet.

He has just begun a study on the Big Hole’s insect environs, although there is not enough historical data on the river to compare the past to this year. So far, he said, the number of salmonflies and other insects in the area seems robust. “The decline in trout,” he said, “is not food-related.”

Still, salmonflies are less prevalent throughout the West than they once were, he noted, vanishing from the Logan River in Utah and portions of the Provo River. They have receded or disappeared altogether on 500 miles of river in Montana.

Another climate-related threat to Montana’s fly fishing is the appearance in some rivers of invasive small mouth bass, a warm water species that prey on trout and could decimate fisheries. State officials have proposed emergency regulations on the Bitterroot River, for example, that require anglers to kill and report any small mouth bass they catch.

A few other potential problems have been mentioned. Some trout have developed proliferative kidney disease. And runoff from battling wildfires over the years with the use of flame retardant containing ammonium phosphate, has been shown to be toxic to fish.

As research continues, Mr. Fellin said his family and the fishing guides he employs have changed their practices to adapt to the river’s changes, trying to aid in the recovery of both the Big Hole and its renowned trout.

“The state says 73, but we stop fishing at 68 degrees, pinch barbs and leave spawning fish alone,” he said. “We owe it to the resource to keep these wild animals alive.”