As Colorado’s native fish struggle, wildlife scientists are working to make their lives easier

Let’s begin where the rivers do: high in the Rocky Mountains, where clean, cold streams form and flow downhill, eventually feeding the state’s largest rivers. This is the realm of Colorado’s poster fish, the cutthroat trout. Colorful, beautiful and beloved by anglers, cutthroats — recognizable by the iconic red slash markings under the jaw that give the species its name — live in the headwaters of almost every river basin in the state. Cutthroat trout are at home where there’s oxygenated water, gravelly bars for spawning, and good vegetative cover on stream banks.

“Cutthroat trout” isn’t just one type of fish in Colorado, but rather, six. There’s the greenback cutthroat trout, originally from the South Platte River Basin on the east side of the Divide. The yellowfin cutthroat came from the Arkansas River Basin, but is now considered extinct. Moving southwest, the Rio Grande cutthroat rose from the Rio Grande Basin. Then, on the Western Slope, the Colorado River cutthroat is further divided into three lineages: the Green River lineage, found in the Green, White and Yampa rivers; the Uncompahgre lineage, of the Dolores, Gunnison and Upper Colorado rivers; and the San Juan lineage, of the San Juan River Basin.

That’s not to say the average angler — or indeed, the average fish biologist — can tell the cutthroats apart just by looking at them. Nor can they be identified based on where they’re caught these days. Humans, from regular people trying to create new fishing opportunities to professional fisheries managers, spent much of the last couple of centuries moving cutthroats around the state with little understanding of the differences between subspecies. “It’s really hard to put the genie back in the bottle once that happens,” says Jim White, southwest senior aquatic biologist for Colorado Parks and Wildlife (CPW). “One of the great mysteries in cutthroat trout distributions was, what went where? What did these river basins look like before we started widespread stocking of cutthroats and non-natives?”

Biologists didn’t know the answer until 2012, when a landmark study led by University of Colorado Boulder researchers conducted DNA analysis on museum fish specimens gathered at the beginning of European contact with the West. Those results confirmed the existence of the six genetically distinct types of cutthroat — five previously known to science, and one brand-new one, the San Juan lineage trout. The study speculated that San Juan cutthroats had also gone extinct, but CPW biologists had to be sure. “We beat the bushes, surveyed all the populations, and conducted molecular tests on fin clips from all known cutthroat trout populations in the San Juan Basin,” says Kevin Rogers, CPW aquatic research scientist and co-author on the 2012 genetic study. “Indeed, there were about a half-dozen populations that [matched] the fish that had been collected in the mid- to late 1800s.”

One thing all five remaining Colorado cutthroat varieties have in common is a reduction in the amount of habitat they occupy. The state’s cutthroats are now relegated to just 12% of their historical habitat on the high end, down to half a percent on the low end, says Boyd Wright, native aquatic species coordinator with CPW. “Most of the lower elevations have been invaded by non-native trout, so cutthroats are persisting only in the headwaters,” Rogers says. Greenback cutthroats are federally listed as threatened, and Rio Grande and Colorado River cutthroats (occupying just 12% and 11% of their historic habitat, respectively) are state species of special concern. The culprits? What began with pollution, overharvesting and the stocking of non-native fish in the era of Western colonization continues today.

Non-native fish pose a major threat to native cutthroats, particularly the brown, brook and rainbow trout that have been stocked statewide and now thrive in Colorado’s waters. “To sum it up, there’s hybridization, there’s predation, and there’s competition,” White says. “All of those three things can interact to disadvantage our native fish populations.” Rainbow and cutthroat trout can breed, resulting in the hybrid cutbow. Non-native trout sometimes even eat the natives. They also compete with cutthroats for food, and often win. Brook and brown trout spawn in the fall and hatch in the spring — so when the cutthroat fry hatch in late summer, their non-native rivals have already had several months to grow bigger.

Climate change isn’t helping. “We have the two ugly stepchildren that come along with a changing climate: drought and wildfire,” Rogers notes. “The toll wildfire can take on cutthroat is substantial. The debris flows that invariably happen afterward can wipe out populations.” Drought can also lower or dry up streams, further contracting ranges.

But CPW and partner organizations like the U.S. Fish and Wildlife Service are actively working to conserve Colorado’s native cutthroats. Biologists raise the trout in hatcheries for stocking back in their native streams, but there’s a lot more to it than that. First, managers must prep the waterways by removing non-native trout, often by poisoning with natural fish toxicants, a process that can take years. Any present pathogens, like whirling disease, must be eradicated. Managers also have to make sure non-native fish can’t reinvade the stream, usually by building a barrier, like a waterfall. Despite the difficulty and expense, the state is actively working on recovery projects for all five cutthroat varieties. “That’s what we’re about, trying to preserve diversity for future generations to enjoy,” Rogers says.

Desert Rivers

As the mountain streams follow gravity into the western lowlands, they flow into larger networks: Rivers like the Yampa, White and Animas feed the desert arteries of the Green and San Juan, and these, together with the Gunnison, Dolores and others join the Colorado. The entire basin touches seven states, from Wyoming and Colorado up north to Arizona and California in the southwest.

The cold swift headwaters give way to rivers that historically swung between huge springtime floods and slow, turbid flatwater. And the trout give way to large, long-lived fish with bodies suited to big water and wild rapids.

Just over a dozen fish species evolved with the chops to survive in the larger rivers within the Colorado River system. Three of them, called just “the three species” by biologists, are the flannelmouth sucker, bluehead sucker, and roundtail chub. These omnivorous swimmers persist in today’s rivers, though managers keep a close eye on conserving their populations so that they don’t go the way of four other native species.

These four — all federally listed as endangered or threatened — have struggled in the face of drastic, human-caused changes to their habitats. The bonytail, a large-finned, skinny-tailed omnivore, is the worst off, with no sustainable wild populations left. Its relative, the humpback chub, sports a pronounced bump behind its head, all the better to stabilize the fish in whitewater. Its populations have stayed stable over the past few years, with most of them found near the Grand Canyon, and the species was downlisted from endangered to threatened in 2021. The Colorado pikeminnow, a powerful swimmer shaped like a missile, is the largest minnow in North America. It can migrate 200 miles annually and lives 40 years or more. Its numbers are slowly increasing in the Upper Colorado and San Juan subbasins, but are declining in the Green River. And the razorback sucker, a bug- and plankton-eater, features a similar keel behind its head that helps it maneuver through high flows.

All four populations have crashed in response to human water use and reduced water availability resulting from drought and climate change, which has altered the habitats they once inhabited. “We have cross-basin diversions that feed water from the Western Slope over to the Front Range,” says Jenn Logan, native aquatic species manager for CPW. “We don’t have the volume of water that we used to see in the spring. With dams and water going into ditches and filling reservoirs, runoff is nowhere near where it used to be. We don’t have sandbars formed in the way that we used to, and these systems relied on sediment to form complex habitats.” Not only that, but dams change water temperature, with released water alternately cooling or warming the river downstream depending on where in the reservoir it comes from. And of course, they form a physical barrier for fish that evolved migrating through a huge, interconnected river system.

Then there’s the non-native interlopers — primarily smallmouth bass, northern pike, walleye, and green sunfish — all introduced, either purposely or accidentally, by humans looking for expanded angling opportunities. “They’re predatory species — they get in the river and can really compete with and consume the native fish in the Colorado River,” says Josh Nehring, deputy assistant director, aquatic branch, of the CPW fish management team. All have found happy homes in the modern Colorado River Basin with its dams, reservoirs and warmer waters.

But just as in the mountain streams, fisheries managers on the Western Slope are working aggressively to protect the natives. The Upper Colorado River Endangered Fish Recovery Program and the San Juan River Basin Recovery Implementation Program oversee the recovery of the four fish species listed as threatened or endangered. The recovery programs are coalitions of water users, federal, state and tribal agencies, plus nonprofits and energy organizations. They take steps like installing nets at the edge of reservoirs to keep non-natives contained and stocking sterile non-native fish in reservoirs to keep them from establishing a population if they do get out. Other work looks like electrofishing stretches of river — that is, introducing a current that stuns fish in the water — and physically removing the non-natives, leaving the native fish to recover and swim another day; and gillnetting northern pike in their springtime spawning habitats. Water managers go so far as to recontour river channels on the upper Yampa to cut off access to northern pike’s spawning wetlands.

Dam management is another useful tool for both helping native fish and disadvantaging the non-natives. The Upper Colorado River Endangered Fish Recovery Program works with the U.S. Bureau of Reclamation at Utah’s Flaming Gorge Dam on the Green River on timed releases — releasing water when biologists detect the year’s razorback sucker larvae “to attempt to move them down to their wetland habitats,” Logan says. They’ll release water to disrupt smallmouth bass nesting, when possible. And in the Lower Basin downstream of Lake Powell, managers have begun releasing cooler water specifically to make the Colorado River there less hospitable to smallmouth bass. As long-term drought has dropped water levels in Lake Powell, “We’ve been seeing increases in water temperature releases coming through the dam,” says Ryan Mann, aquatic research program manager for the Arizona Game and Fish Department. Some smallmouth bass made their way into the river below the dam in years past, but the water had been cold enough to keep them from reproducing. But in 2022, biologists found baby bass. Last summer’s cold-water releases prevented widespread spawning, and managers may continue them into the future.

Today’s Colorado River Basin is a radically different place than in centuries past, and, “Unless there’s some amazing technology that comes along to remove all non-native fish or a way to return flows to historic conditions we’re not going to be able to move [major river systems] back to native fish,” Nehring says. But that doesn’t mean those species are doomed. CPW and its partners are actively raising threatened species in hatcheries and reintroducing them to targeted habitats. “We’re really focusing on the tributaries, to keep the natives alive in enough areas where we know they’ll persist,” Nehring says.

Eastern Plains

As alpine streams flow east, they meander through Front Range cities, then spread across the arid plains. The water warms, rocky beds grow sandy, and habitats shrink as creeks dry up seasonally. Waters dominated by a single species explode with different fish. “We’ve got this melting pot of biological diversity along the transition zone,” says Wright. “You go from historically a one-species profile in the mountains to more than 28 as you go farther east. These [plains] are very harsh, unpredictable environments.”

The fish that evolved to thrive on the plains, from the region’s western edges in Colorado out into Kansas, Oklahoma and Nebraska, are largely the opposite of the big, long-lived species on the Western Slope. They’re a few inches long, live just a couple of years, and reproduce early. These fish are used to biding their time in small pools until rain or spring runoff reconnects the intermittent creeks, finally allowing them a change of scenery.

But the Eastern Plains haven’t escaped the challenges affecting Colorado’s other rivers — its native fish are struggling, too. “Most of our plains fishes are declining or locally extinct because of habitat modification or loss,” says Ashley Ficke, fisheries ecologist with engineering firm GEI Consultants. Humans have diverted water to farms and municipalities, redirected streams into straight channels lacking habitat complexity, and even drained some waters completely. That hits fish like the plains minnow particularly hard, as its semi-buoyant eggs float vast distances between spawning grounds and ideal nursery habitat. “It needs vast portions of unfragmented stream habitat,” Wright says. “We’ve really lost that in Colorado, and that’s a big reason why they’re very rare.”

As elsewhere in the state, though, fish managers are working to replenish the swimmers of the plains. At a hatchery in Alamosa, CPW breeds 12 rare native fish, half of them eastern species: plains minnow, suckermouth minnow, northern and southern redbelly dace, Arkansas darter, and common shiner. “We’re working with private landowners that have streams or ponds that would be suitable for these native fish, working with them to maintain or improve that habitat, and stocking those waters with the native fish,” Nehring says. By preserving and restoring enough of the plains’ stream habitats, managers hope to give back sufficient waters for these little fish to persist.

This article first appeared in the fall edition of Headwaters magazine.