In Montana, fly fishermen are watching a bleak trend.

The number of brown and rainbow trout in some of the state's best known and most scenic fishing rivers is at historic lows.

And experts are at a loss to explain it.

State agencies, fishermen, businesses and concerned citizens are all trying to find answers.

Montana PBS is Joe Lesar takes us to southwest Montana for a deeper look.

JOE LESAR (voice-over): For the past 39 summers, Craig Fellin has run the Big Hole Lodge, guiding anglers on Southwest Montana's world class rivers.

This area is the state's fly fishing Mecca, and it's where Craig passed down his love of the sport to his son Wade.

WADE FELLIN, Co-Owner, Big Hole Lodge: For the past 17 years I've been a guide at Big Hole Lodge and working alongside my father, JOE LESAR (voice-over): Craig and Wade now co owned the lodge, which sits about eight miles from its namesake, the Big hole River.

Nicknamed the last best river.

It supports the last naturally producing population of fluvial Arctic Grayling in the lower 48 states.

WADE FELLIN: And it's beautiful.

Its pristine, with a river running through it with wild trout.

JOE LESAR (voice-over): Four Species of Montana's wild trout caught this river home drawing anglers from all over the world.

WADE FELLIN: You can spend eight hours and not have thought of anything other than where fly is in the water column in relation to where a fish might be.

JOE LESAR (voice-over): But something is happening to the fish.

This spring, Montana Fish, Wildlife and Parks released data showing that numbers of brown and rainbow trout are at or near historic lows in certain stretches of the Big Hole.

And the neighboring Beaverhead and Ruby rivers.

Fellin and other guides are seeing it firsthand.

Diseased fish covered in growths and lesions.

And these declines are not simply an environmental issue.

Angling on the three rivers accounts for the lion's share of the county's $167 million outdoor recreation economy.

WADE FELLIN: I had a client leave two weeks ago and say good luck with all of this.

I hope you figure it out.

I hope we can come back someday when it fishes better.

We really struggled this week.

JOE LESAR (voice-over): The Fellins believe they have a responsibility to help preserve these rivers.

WADE FELLIN: We can't just sit on our hands we have to do something and we feel that it truly is an all hands on deck moment.

JOE LESAR (voice-over): Jim Olson, a biologist for Montana Fish, Wildlife and Parks, says brown trout are typically Montana's most resilient trout species.

And the cause for their decline is still unclear.

JIM OLSEN, Big Hole Fisheries Biologist, Montana Fish, Wildlife and Parks: They should be the one that are doing the best and they're the ones that are our base basically crashing right now.

We don't have the information to be able to say definitively that's what it is.

JOE LESAR (voice-over): What they do know is that several stretches of drought in Montana over the past decade has stressed populations.

Less water that warms up earlier in the year is not ideal for trout, which thrive and strong and cold water.

Experts also point to the possibility of a new disease.

Brian Wheeler heads the Big Hole River Foundation, a nonprofit working to protect the river.

He also works as a fishing guide.

BRIAN WHEELER, Big Hole River Foundation: We're seeing open lesions on the heads what people have started to call that cheese grater heads.

JOE LESAR (voice-over): Wheeler says it would make sense to see sick fish at the end of the summer when water is low.

But that hasn't been the case in recent years.

BRIAN WHEELER: We're not just seeing it in October.

We're seeing it in June, when there's a ton of cold flow in the river.

That is really strange.

It doesn't add up.

JOE LESAR (voice-over): In June, Montana Fish, Wildlife and Parks announced an effort to find answers about the declines.

And in July, fish experts on the Big Hole River did some early electro fishing.

A method researchers use to help them study a sample of the population.

When the electrode hits the water, it creates an electrical current that the fish are drawn to.

The goal is to find sick fish when they're still alive, and collect samples immediately after they're killed.

The quickly preserved samples are sent to specialists to look for signs of disease at the microscopic level.

WADE FELLIN: No one organization is responsible for this and no one organization can quickly solve this.

JOE LESAR (voice-over): This summer, Wade Fellin announced the launch of Save Wild Trout, a privately funded group made up of guides anglers and businesses.

WADE FELLIN: And what save wild trout hopes to do is identify what we feel are gaps in data collection, and privately fundraise bring that data together with expert scientists that can wrap it up in a bow and bring it to the state to help inform their management decisions moving forward.

JOE LESAR (voice-over): And the hope is that all of this research will help protect the larger ecosystem beyond the big holes trout population.

Brian Wheeler runs the Big Hole River Foundation's Water Quality Program.

He's studying how water quality affects trouts main food source.

BRIAN WHEELER: All these issues that we're seeing are not just impacting trout population levels, they're impacting the bugs as well.

JOE LESAR (voice-over): Like the trout in the big hole River, certain aquatic insect species are also in decline across the West.

BRIAN WHEELER: This is like baseline food chain stuff.

And so when you start to see these declines and shifts, you know, it affects everything from there on up.

JOE LESAR (voice-over): It will take a year or two to know for certain if this year is good water conditions helped to reverse the trouts decline.

But further down the road questions remain about the human effect on and responsibility for these fish.

And for Montanans like Craig Fellin, it's a task they're happy to take on.

And one he's confident the next generation will embrace.

CRAIG FEELIN, Founder, Big Hole Lodge: Where it is going to take over here and I'll be able to go fishing a little more.

JOE LESAR (voice-over): For PBS News Weekend, I'm Joe Lesar in Wise River, Montana.