Bringing Back the Cutts

For 30 years, scientists have been waging a struggle to control invasive lake trout in Yellowstone Lake, trying to curb their numbers before they completely destroy what was once the largest population of Yellowstone cutthroat trout in the Intermountain West. I wrote about this effort in “Science in the Thorofare: The Story of Yellowstone Cutthroat Trout #4089” in the Feb.-Mar. 2024 issue of Fly Fisherman.

That story recounted a trip with Yellowstone National Park biologists, including Dr. Todd Koel, Yellowstone’s lead fisheries biologist and the primary person responsible for managing the lake trout problem. We fished the headwaters of Yellowstone Lake, a roadless region known as the Thorofare where increasing numbers of Yellowstone cutthroat trout continue to spawn each spring, doing their part to save their species from lake trout annihilation.

But most anglers will never experience this fishing. Unless you’re able to hike more than 30 miles into grizzly bear country carrying all your supplies on your back, or willing to endure the expense and saddle sores from hiring an outfitter to get you there on horseback, the Thorofare will remain beyond reach. It’s the stuff of unfulfilled bucket lists.

But there’s another way to catch these trout. Just as the Yellowstone River flows into Yellowstone Lake from the Thorofare, it also flows out of it. Yellowstone Lake and the Yellowstone River upriver from its upper falls harbor the same fish population as the Thorofare region. These fisheries are also experiencing a population surge of large, native Yellowstone cutthroat trout—largely from the success in controlling and reducing the predatory lake trout population. It’s not often that the fishing in a river and lake that have been world-famous for well over 100 years dramatically improves, but that’s exactly what’s happening. And unlike the Thorofare, here you can access both the lake and the river from your car.

Lake Trout Mystery

How piscivorous lake trout came to inhabit Yellowstone Lake is still a mystery. What we know for certain is that the lake provides some of the best lake trout habitat on Earth. Its blue water is deep and cold, concealing rocky, stone-cobbled reefs that offer ideal spawning sites. Yellowstone cutthroat trout evolved in this inland sea without subsurface predators, so they are ill-equipped to avoid the voracious appetites of lake trout.

The first verified lake trout was caught in 1994, though rumors of their existence began in the 1980s. Authorities and anglers at the time were quick to blame fishermen for introducing the lakers from nearby Lewis and Shoshone lakes, where they were first stocked by the U.S. Fish Commission in the 1890s. But imagine what would have had to take place for anglers to establish lake trout in Yellowstone Lake.

First, lake trout needed to be caught—males and females. Then they had to be kept alive while more were caught—you couldn’t illegally stock one or two and expect them to overtake a lake of Yellowstone’s size. The captured fish had to be transported, alive, to somewhere along, or within, Yellowstone Lake where they would be released, on multiple occasions, without anyone seeing this happen. Maybe it was done at night? But you’re not allowed to fish in the park after sunset.

It is still possible that immoral anglers illegally placed lake trout in Yellowstone Lake—fishermen have intentionally introduced nonnative species in other locations in the United States. But I believe it’s unlikely that one person, or even a few people, successfully did this. In the late 1800s, Atlantic salmon and rainbow trout were intentionally stocked into Yellowstone Lake by fisheries professionals, and those efforts failed. But these unknown 1980s scofflaws somehow succeeded with lake trout? Perhaps you count criminal masterminds among your angling friends. I once watched with amazement, for 10 minutes, as two of my dissimilarly sized friends unknowingly struggled to fit into each other’s waders.

Yellowstone National Park supervisory fish biologist Dr. Koel has another hypothesis. He believes that lake trout may have entered Yellowstone Lake “naturally” by swimming into Yellowstone over the Continental Divide from Jackson Lake. I’ve been to the Thorofare region after peak runoff subsided, and even then, it’s very wet. During heavy runoff, it’s possible that lake trout found their way into Yellowstone Lake through the flooded region.

Dr. Koel has provided strong evidence that his hypothesis is possible by using environmental DNA (eDNA) sampling, in which water is tested for the DNA signatures of various fish species. He found lake trout eDNA in waterways that could connect other lake trout–inhabited lakes in this region to Yellowstone Lake during high-water events. Here’s Koel, writing in the June 2020 edition of the journal Water: “The original assumption that lake trout were introduced illegally was based on the belief that they could not have moved into Yellowstone Lake from other park waters on their own. We now know that assumption was incorrect.”

But how we got here is largely an academic question. Where we are now, and where we’re going, is what really matters.

Predatory Lakers

Before lake trout arrived in Yellowstone Lake, the lake and the Yellowstone River flowing out of it were full of Yellowstone cutthroat trout. Fishing Bridge, at the outflow of Yellowstone Lake, was internationally famous for its cutthroat trout fishing.

My friend Matthew Long, who spent his childhood summers fly fishing the park, told me that during his best day on the Yellowstone River below the lake he caught 130 Yellowstone cutthroats. Then lake trout appeared. As their population grew, the cutthroats crashed, falling to the point where 90 percent of their spawning population was wiped out. Fewer people fished the upper Yellowstone River after that because there weren’t many fish to catch.

Yellowstone National Park began a rudimentary gillnetting program in the mid-1990s to remove lake trout, but data soon revealed that it wasn’t nearly enough to limit the invaders, and lake trout numbers continued to explode. This is when Dr. Koel and his team were given control of the effort to save the Yellowstone cutthroat trout. Over a 17-year period, a multimillion-dollar professional gillnetting operation was developed, greatly expanding the number of nets in the water. Approximately 4.75 million lake trout have been removed from Yellowstone Lake in the past three decades.

Koel and his biologists also began attacking lake trout spawning areas. Their methods have evolved over the years as new data has been compiled and studied. One reduction method uses a helicopter to spread plant-based pellets onto the spawning sites. The force generated by the rotors slams the pellets into the water, driving them subsurface and allowing them to quickly reach the bottom and smother the lake trout eggs, which die as the decomposing pellets remove oxygen from the immediate area.

Because of these combined efforts, adult lake trout numbers have drastically declined, to the point where the cutthroats can now prosper in spite of them. Dr. Koel’s multifaceted plan has worked: The average lake trout in Yellowstone Lake today is younger, smaller, and less capable of eating cutthroat trout. We now know that lake trout will most likely never be eradicated from Yellowstone Lake. But their population can be limited to allow Yellowstone cutthroats to survive and flourish as well, and the cutthroats are staging an improbable comeback. This is what success looks like.

Fishing the Lake

In 2024 I was invited to join Todd Koel and his son Tyler on a Yellowstone Lake fishing trip. We hoped to catch Yellowstone cutthroat trout, but we also knew there was a chance we could encounter lake trout and play our legally mandated role to remove them. We caught lots of cutthroats that day—heavy golden bronze and blood-red fish. We also caught nine lake trout.

As I began filleting the first laker, the pressure of my knife against the fish’s flesh caused two small prey fish to pop out of its mouth—young-of-the-year cutthroat trout. I’m a hunter, and I’ve eaten my share of fly rod-caught trout over the years. Though I’ve never taken pleasure in the killing aspect of hunting and fishing, that moment made me glad that these lake trout could never again encounter a Yellowstone cutthroat.

Yellowstone Lake is a dangerous place. Its water temperature is frigid even in the hottest part of summer, so anglers must wear life vests while boating. Storms often appear over the majestic, snow-crowned mountains that rim the water, instantaneously changing a bluebird day into a windy, wave-pounding mistake. This is no place for your drift boat. Some anglers skirt the shoreline in kayaks or belly boats, but to get safely to, and from, the lake’s open water you need a bigger boat, something stable, with an engine.  

If you don’t have your own boat, you can hire a guide or rent a boat from Yellowstone’s primary authorized concessioner, Xanterra. Or you can fish from shore along the West Thumb and Gull Point Drive, around Carrington Island, or near the Bridge Bay and Grant Marinas, though small sections of all these areas are permanently closed to fishing. Always consult the Yellowstone Fishing Regulations to make sure you’re fishing legally.

Fishing from shore is a great way to catch some of Yellowstone Lake’s cutthroat trout. Throughout the summer and fall, they cruise shallow areas, searching for mayflies, caddisflies, midges, damselflies, and dragonflies. The lake also contains an enormous population of olive-colored scuds, so many that they are even eaten by adult lake trout. Dry/dropper techniques with a Chubby and a Perdigon nymph or olive scud are effective when the trout aren’t rising, and it’s hard to beat a size 12 or 14 Yellow or Purple Haze or a standard or Parachute Adams when they are. Standard 9-foot 3X leaders will usually suffice. Look for rising fish cruising the shallows and cast your fly (or flies) in the direction they’re headed. Make sure you bring your waders and warm underlayers. You cannot wet-wade this icy water for very long, even on the warmest day.

If you do bring your own boat, National Park Service staff will need to inspect it for invasive aquatic organisms before it’s allowed to enter the water. The park has very specific guidelines for using watercraft on Yellowstone Lake. Make sure you read them on Yellowstone National Park’s official website well in advance of your trip.

If you want to catch lake trout, use 10-foot, 6- to 8-weight fly rods paired with fast-sinking fly lines to strip streamers such as Woolly Buggers, Sparkle Minnows, or other patterns resembling Yellowstone cutthroat trout. Usually you’ll want to spend most of your time casting to water that’s at least 10 feet deep to have a chance at the lakers. But in the fall you can find them in shallower water along one of their main spawning areas at Carrington Island.

Above the Falls

Prior to the 2024 Yellowstone fishing season, I hadn’t fished the Yellowstone River downriver from Fishing Bridge for more than 10 years. There weren’t many fish, so I avoided the area.

In 2024, Dr. Koel told me that he’d received multiple reports of anglers catching tagged Yellowstone cutthroat trout in this section of the river. Any fish with Floy tags must have been previously captured in trap nets in Yellowstone Lake to receive the tags. And cutthroats caught out in the lake are generally quite large.

Koel asked me to take members of the Yellowstone Fly Fishing Volunteer Program (YFFVP) to the river to see what we could find. The YFFVP is one way biologists can gather data about the health of fisheries within the park.

On our first day, we walked the river along a deep pool, looking for trout. Eventually we saw a rise, then another and another. There were a smattering of PMDs on the water, and the fish were eating them. We caught a dozen heavy Yellowstone cutthroats that day and hooked many more. But fish in the 18- to 24-inch range are difficult to land in water as expansive as the Yellowstone River, where the forceful push of the river, combined with abundant misshapen rocks, makes wading difficult. Despite the challenges, it was immediately clear that the Yellowstone River once again holds a robust population of large cutthroats that spend at least part of the year in Yellowstone Lake.

It can be confusing to figure out where you’re allowed to fish the river because several stretches are closed to fishing, and there aren’t always signs to tell you exactly where those boundaries exist. Again, always consult the Yellowstone National Park fishing regulations. The lowermost open water above the falls begins at the Chittenden Bridge. You can fish from here to Alum Creek, which enters the river in the Hayden Valley, but the next 6 miles are closed to fishing to create a trout sanctuary and a pristine wildlife viewing area.

Fishable water returns just upriver from the Sulphur Caldron/Mud Volcano area and continues upriver to LeHardys Rapids, but you’re not allowed to fish 100 yards below or above the rapids.

Fishable water extends from above LeHardys to 1 mile below Fishing Bridge, where it’s closed to protect a large cutthroat spawning area. You can begin fishing again a quarter mile above Fishing Bridge.

This part of the Yellowstone River is often wide and slow-moving, which can be challenging for some anglers. If trout aren’t rising, concentrate on the heads and tails of deep pools. Also, look for depressions in the riverbed; these “buckets” often hold fish. The sections with riffles and runs can be good, as long as the water is at least a foot or two deep. Fish these areas with hatch-matching patterns early in the season, which opens July 1.

The river sees the same general hatches as other park rivers and creeks. But the slow pools also create habitat for Callibaetis mayflies, which are more often found in lakes and ponds. Fish dry/dropper rigs with size 10 or 12 Chubbys as your lead fly, nymphs under an indicator, or strip black or yellow streamers and swing wet flies through likely holding areas.

My most productive nymphs have been black and tan mottled Pat’s Rubberlegs and Perdigons with a pheasant tail, metallic blue, or green body and a red or orange hotspot.

In the fall, before the Yellowstone River fishing season ends on October 31, the fish feed heavily as they stage in various locations, most likely gathering for a return to the lake. Some days you can watch fish swimming past you as they migrate upriver. I’ve also stood on the precipices of drop-offs and had pods of fish bump into my legs as they searched for food and navigated pathways toward the lake. I’ve witnessed this exact behavior from my days guiding rivers and creeks that drained into the Great Lakes.

As winter descends upon the park, the lake and the river grow quiet, though the struggle to save this fishery continues, as the previous season’s data is processed and scrutinized. There’s much more to do. But Dr. Todd Koel and his team of scientists are winning the struggle to save the Yellowstone cutthroat trout. Take a drive and see for yourself.

Paul Weamer is the author of Favorite Flies for Yellowstone National Park (Stackpole Books, 2022) and Dry Fly Strategies (Stackpole Books, 2021). He is a program coordinator with the Institute on Ecosystems at Montana State University, and runs the Yellowstone Fly Fishing Volunteer Program. His most recent story for Fly Fisherman was “The ‘Other’ Natives: Restoring Yellowstone’s Westslope Cutthroat Trout and Arctic Grayling” in the April-May 2025 issue.

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