The San Rafael River has a problem. As it winds through red rock country northwest of Canyonlands National Park, it increasingly runs dry.
Drought is again taking hold across Utah, and that could spell trouble for the wildlife that rely on the river, such as native fish that get stranded in puddles when the flow stops.
“Picture being in a little pool and never being able to move. Your oxygen levels start to get low. Your temperature starts getting higher,” said Tyler Arnold, an aquatic ecologist with the Bureau of Land Management’s Green River District. “So, you've got multiple things working against those fish to be able to survive.”
It’s a growing problem, Arnold said, with the small Colorado River tributary going dry more frequently and for longer periods than it did historically. During Utah’s 2020 drought, for example, the stream gauge near State Route 24 in Emery County recorded no flow for roughly six weeks straight.
Fifteen years ago when Utah State University watershed sciences professor Phaedra Budy began to study the river, small sections would dry up occasionally.
“Now, there are years where the entire lower 40 kilometers of the San Rafael are completely bone dry.”
Even for hardy desert natives, there’s only so much they can take.
“These fishes have evolved over millions of years to deal with extreme drought and extreme flood,” she said. “The problem in places like the San Rafael is that this extreme drying is happening more often and to a much greater extent than it would have over their evolutionary history.”
Across the Colorado River Basin, growing cities and thirsty farmland continue to fight for pieces of a shrinking pie, and there often isn’t much leftover for ecosystems.
Part of the problem is the basin’s water rights were divvied up at a time when the climate was cooler and wetter than it is now. So today, a lot of that water only exists on paper. As far back as 2000, the state of Utah described the San Rafael as “the most over-appropriated drainage” in its region of the basin.
“Now in light of drought and climate change, we simply are seeing more overallocation and more demand for water,” Budy said. “And more fights between humans and fish for this very, very precious resource.”
Overuse has also transformed how the river looks. Because so much of it is being dammed and diverted for farms, towns and industries upstream, Budy said there is no longer a snowmelt flood in the spring.
That annual rush of water generated the complexity of the river’s historically diverse flow patterns. The channel would split into braided streams on the flood plain and create a variety of habitats that fish love, from calm deep pools used for refuge to rocky riffles used for feeding. Today, however, much of the San Rafael appears more like a homogenous canal than a diverse refuge — when it has enough water to flow at all.
The changes over the past few decades have led to a dramatic decline in native fish populations. Some species, like the flannelmouth sucker, bluehead sucker and roundtail chub are endemic to this region and found nowhere else in the world. They rely on small tributaries like the San Rafael for safe places to feed, rest and reproduce. All three species are protected in Utah.
If they disappear, that’s a canary-in-the-coalmine moment for the whole river environment.
“Fish in particular are indicators of ecosystem health,” Budy said. “So, if you have a healthy native fish population, it tells you that you have a healthy ecosystem.”
By 2009, these native fish were found in just half of their historic range. Some species have now seen range declines up to 85%, Budy said.
The magnitude is so great that she worries Utah is not making large enough strides to turn that tide. With federal funding freezes and the Trump administration’s push to limit spending on environmental efforts, she’s concerned the small existing restoration projects could see some of their support evaporate, too.
One potential solution could be to buy upstream water rights from farmers and ranchers who are leaving agriculture, she said, but that requires a willing seller and a chunk of cash. State leaders have taken some steps to help water rights holders leave more of their allocation in the stream, but it can still be a complex process that takes time to pay off.
In the meantime, scientists are testing out ways to adapt the river to its new, drier reality.
“We're not getting the water regime back that we had historically,” said Cassie Mellon, who leads the aquatic resource program with the BLM in Salt Lake City. “So, we need to figure out what we can do with the current water regime and the expected water regime to maintain something for these rivers.”
On a bank of the San Rafael in Emery County, Mellon and Arnold pointed out some of that work in action. A line of wooden poles peak above the shallow water with branches tangled behind them, forming a loose dam.
It’s an example of a post-assisted log structure, meant to mimic how beaver dams and natural debris historically shaped the river’s flow. As water is forced to go around it, that can help recreate some of the plentiful dips and pools that fish thrived in years ago.
“That's the question we're trying to answer,” Arnold said. “Will these man-made structures that we're creating hold fish during periods of low flow?”
The structures aren’t meant to be permanent. The idea is for beavers to take over as the river regains some semblance of its former self.
A nearby spot shows the potential.
In 2010, a natural sediment plug blocked the main channel, causing it to spill out into the floodplain. In response, scientists saw beavers return on their own and achieve restoration results beyond what man-made projects have accomplished. By 2021, riparian habitat along that stretch had increased by 230%, and it had the most diverse flow patterns of anywhere on the river.
For the people trying to give these native ecosystems a better future, it offers some hope that the San Rafael and its wildlife aren’t beyond saving.
“These fish are tough,” Mellon said. “If we can just give them half a chance, I think they will come back.”
