Replenishing the San Juan River

A tribe’s change of course has ripple effects for endangered fish species

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>>This story was funded by a grant from The Water Desk, a project of the Center for Environmental Journalism at the University of Colorado Boulder. waterdesk.org Hear an audio version on KUNM.org.<<

On an unseasonably hot July day, Jerrod Bowman peers into the water flowing through a box-like passage for endangered fishes, checking their route is clear. Bowman works as a fish biologist for the Navajo Nation, based west of Farmington, where the San Juan River borders the reservation. A small dam here forms a barrier to the seasonal migration of two rare fish species, the razorback sucker and the Colorado pikeminnow. On the south side of the river a narrow, rocky channel leading to a concrete bypass serves as a passage around the dam.

“I’m just trying to give them the chance to move upstream,” Bowman says.

Historically, Colorado pikeminnows traveled hundreds of miles through the free-flowing rivers of the Colorado River Basin, from Wyoming to northern Mexico. Razorback suckers also migrated seasonally to spawn through a similar range.

Today, after a century of dam-building and other human intervention, the fishes are restricted to 25% of their historical range. Both nearly became extinct in the San Juan River. Now, with climate change drying the river, the federal, state and tribal partners responsible for the fishes’ recovery are hopeful about a new opportunity to keep the water flowing.

At the dam, an olive-colored waterfall spills over a wide concrete weir. This diversion once conveyed 1 million gallons of water per hour uphill to cool the now-decommissioned San Juan Generating Station, a coal-fired power plant. Public Service of New Mexico (PNM), the utility that operated the plant, leased the water from the Jicarilla Apache Nation.

A landmark agreement signed last year means the water is being put to a very different use—to help the fishes. A novel partnership and a unique state program made the pivot possible, creating revenue for the Jicarilla Apache Nation, a potential solution to the state’s water obligations, and hope for a river and fishes on the brink.

For seven years, Bowman has been a biologist for the Navajo Nation, where he works to help native fish species get past the so-called PNM dam, while keeping nonnative fishes out. Formerly, biologists closed the passage, trapping the fish, then sorted native species from nonnatives before releasing them upstream. Invasive fishes like channel catfish are major predators for the endangered species throughout their range. Now water managers have opened the passage completely, letting the fish travel through on their own.

On this afternoon, Bowman is troubleshooting a new addition to the passage, an infuser that pumps additional oxygen into the water, “trying to get them enticed to use the fish passage all the way up.”

The Endangered Species Act requires state and federal river managers to address the fishes’ sharp decline over the last century, though the Fish and Wildlife Service proposed delisting the razorback sucker in 2021. Bowman and other biologists with the San Juan River Basin Recovery Implementation Program work on restoration and monitoring, as well as rearing fish.

Bowman uses underwater antennas that detect tiny tracking tags, among other methods, to monitor fish..

“Right now, our numbers have been some of the best numbers we’ve had for a long time,” he says.

It could be the opened passage or the oxygen infuser drawing the fish upstream. But the recent influx of water also makes a critical difference.

In June, a torrent of water surged out of the Navajo Dam into the San Juan River. Over several days, a spring pulse of over 24,000 acre-feet of water scoured the San Juan’s sandy banks and gravelly riverbed, mimicking natural snowmelt runoff.

The high flows washed out sediment and opened up secondary channels for fish to use for breeding, Bowman says. “It’s been a long time since I’ve seen water that high.”

When he was a kid in Shiprock in the late 1980s, Bowman would swim in the deep, slow water of the secondary channels. “We could go in there and swim all day,” he says. “You didn’t even touch the bottom.”

Then the channels dried up because of drought. With the spring water release, some of his old swimming holes are open again, he says.

The San Juan’s seasonal floods from winter snowmelt and summer monsoons ended once the Navajo Dam, finished in the 1960s, and other small dams built for flood control and irrigation were built. The dams here and elsewhere in the Colorado Basin forever altered the system’s ecology, ending the great migrations of the basin’s endemic fishes.

The reservoir behind Navajo Dam, about 50 miles upstream from the PNM dam, is popular for recreation by boaters, though its main purpose is water storage and flood control—including as the location where the Jicarilla Apache Nation stores most of its apportioned water.

The water newly reallocated to replenish the river comes thanks to a historic partnership between the state of New Mexico and the Jicarilla Apache Nation. The tribe is leasing up to 20,000 acre feet of water per year to the Strategic Water Reserve, a state program that works like a savings account for water rights.

When PNM decommissioned the San Juan Generating Station, the Jicarilla Apache Nation was suddenly left without a client for most of their Colorado River Basin water rights—and their revenue stream. At that time Daryl Vigil was the water administrator for the nation. He explains that per the tribe’s 1992 settlement, the bulk of their water travels from the Colorado River Basin to Navajo Reservoir, located dozens of miles from the Jicarilla reservation, making it cost-prohibitive to pump there.

Instead, the tribe leases the water, which supports government operations, Vigil says. “It’s a huge amount of income.” Yet rather than being put to a use that benefited the tribe, Vigil says for several years it was “just going down the river to prop up lake levels at Lake Powell,” a large downstream reservoir on the Colorado River at the Utah/Arizona border.

Major obstacles kept the tribe from quickly finding a new lessee for its water. For example, laws governing the river made it impossible for the tribe to market water across state lines or participate in conservation programs, Vigil says.

Once Gov. Michelle Lujan Grisham took office in 2019, Vigil says the state became interested in working with the tribe to lease the water using a little-known state tool called the Strategic Water Reserve. Created in 2005, the reserve allows for leases and purchases of water rights for two purposes: complying with interstate compacts and meeting Endangered Species Act obligations.

Despite the interest from the state, the deal took years to complete, and faced significant technical and legal challenges. The state had never entered into an agreement with a tribal nation in this way before. “In terms of a sovereign-to-sovereign transaction in the state of New Mexico,” Vigil says, “we could not find a template for one.” The lease is also the first of its kind on the San Juan River and the largest amount of water ever leased to the reserve.

That record amount of water required a large payment, another complication. The Nature Conservancy stepped in as a key partner, providing technical expertise and fundraising to add to the state’s contribution so the nation received market value for its water, Vigil says. In the end, the tribe received a total of $1.76 million for the lease, with the state paying $650,000 and the Nature Conservancy $1.1 million.

The lease also represents a major new opportunity for New Mexico tribes. Vigil has been working on water issues with tribes in the basin for years, and currently is co-facilitator of the Water and Tribes Initiative. He says tribes have been left out of negotiations on the management of the Colorado River, despite holding over 20 percent of the basin’s water rights. The new lease could have a ripple effect. “Hopefully, it sets the structure and model for other tribes to take advantage of” opportunities for water transactions, or other agreements, he says.

And according to Vigil, the lease to the reserve connects to the Jicarilla Apache Nation’s values. Replenishing the river is “just perfect,” he says, since the nation was a “founding participant” of the recovery program for the endangered fishes.

A few miles from the PNM dam, the Navajo Nation rears razorback suckers in a collection of ponds fed by San Juan water. It’s an oasis of cottonwoods and bulrushes buzzing with dragonflies and flycatchers, surrounded by irrigated fields and scrubland. The nation and its recovery partners grow larval fish to maturity here, then implant them with tiny tracking tags before releasing them into the river.

Biologists reintroduce fish at several sites, including one downriver from the PNM dam. In the shadow of the imposing Hogback ridge and below Route 64′s steady traffic, a small diversion carries water to Navajo farmers who cultivate corn, melons and alfalfa. The diversion was first built in the early 1900s, with a series of improvements made over the century since. Alongside the concrete dam, a deeper channel lined with boulders allows fish to bypass the barrier. Coyote willows line the sandy banks. And across the river, bright green cottonwoods and invasive Russian olive trees shade a heron fishing in the current.

“Historically, the San Juan River was a wide, slow, shallow river,” says Diego Araujo, FWS biologist.

The sharp-keeled razorback sucker and the silvery Colorado pikeminnow evolved over millions of years along the sandy meanders and deep canyons of the river. Toothless pikeminnows could live up to 50 years and grow at least 5 feet long while razorback suckers reached lengths over 3 feet, with life spans up to four decades.

The warm backwaters and eddies on the San Juan’s historical floodplain were critical nurseries for both species, where young fish could feed and mature away from large predators.

“Through manmade constructions and settlement, it has become narrow” and channelized, with colder water and plants crowding the river’s banks, Araujo says.

June’s spring pulse of high water served as an important cue for the fish, simulating seasonal flooding from snowmelt, to “initiate their historical cues to migrate upstream,” he says.

Yet despite efforts by the recovery partners, only a couple wild self-sustaining populations of either species in the greater Colorado Basin remain. Biologists have documented one small razorback sucker population with fish spawned in the wild consistently reaching adulthood, and one population of wild Colorado pikeminnow reaching adulthood in high numbers.

The razorback sucker “are still effectively extinct in the wild in the upper basin,” says Taylor McKinnon, southwest director for the Center for Biological Diversity.

McKinnon says increased river flows aren’t enough to save these two endangered species, but they are a “step in the right direction.” While the fishes are adapted to desert rivers, he says, “the relatively sudden onset of aridification and declining river flows really pose challenges” to species vulnerable from habitat fragmentation and predation.

The long-term outlook for the Southwest is bleak; the region is in the grip of a two-decades-long megadrought. Some scientists argue that, unlike a traditional drought, it’s not temporary. They say the process of aridification, with increased temperatures that dry soils and reduce river flows, marks a transition to a new environment of greater water scarcity.

The San Juan River Basin Recovery Implementation Program established flow targets to sustain the river and keep fish alive, but Fish and Wildlife Service Program Coordinator Melissa Mata, says “they’re getting harder to meet when we’re in these arid drought conditions.” She says the reserve could be a tool to help achieve flow goals. But not all years will be like 2023, with high water due in part to record snowpack and natural flows from undammed rivers like the Animas, which joins the San Juan in Farmington. Under drought conditions, she says, instead of creating replenishing floods, the water from the lease would support base flows, the minimum amount of water needed to maintain fish nurseries.

The expense of water leases and purchases presents a major challenge for the reserve, especially in high-demand river systems like the San Juan and the Rio Grande, where water purchases and leases can run into the millions of dollars.

Yet state lawmakers have underfunded the Strategic Water Reserve, according to the New Mexico Water Policy and Infrastructure Task Force, a group convened by the Office of the State Engineer last year.

Interstate Stream Commission Director Hannah Riseley-White says the lack of consistent funding from the Legislature means the reserve is underutilized.

“Ideally, the state would have a big pot of money that we could use that we could depend on,” Riseley-White says.

“Non-reverting” money, that can’t be clawed back by the Legislature in tough economic times, “would allow us to negotiate significant water rights purchases in other basins, including the Middle Rio Grande. Those efforts take time,” she says.

That means the state has missed out on opportunities. Riseley-White told a legislative committee in February she had to turn down an offer for coveted pre-1907 Middle Rio Grande water rights because of a lack of funds.

In the 2023 legislative session, Sen. Liz Stefanics, D-Cerrillos, introduced a bill to provide $25 million to the reserve. The bill did not advance; instead the reserve received a $7.5 million budget appropriation.

“It sounds like a great amount of money to the public,” Stefanics says. “But it’s really not when you think of all the water settlements and needs that we have in our state.”

Conflicts over the major interstate compacts have proven extremely complex and costly. New Mexico is awaiting approval of a settlement resolving a years-long dispute with Texas regarding the Rio Grande Compact. And while a historic agreement was struck earlier this year between the states of the Colorado River Compact, officials are still negotiating the details.

“Given increasing water scarcity due to climate change, it’s going to be increasingly difficult for New Mexico to comply with our interstate obligations,” Riseley-White says. But the reserve gives the state more control over water deliveries to help meet those requirements, she says.

Adrian Oglesby, director of University of New Mexico’s Utton Center, a natural resources research center, says the reserve provides the state with much-needed flexibility when it comes to responding to crises like the current heat season.

“Doing a water transaction to try to move water someplace where we need to protect something, in the face of these incredible temperatures, that’s just not practical,” he says—it takes years to negotiate water leases. But once water is banked in the Strategic Water Reserve, the state can “manage it creatively.”

Despite being created 18 years ago, the reserve lacks recognition, and not just by the public.

“I don’t believe that many legislators either understand what the Strategic Water Reserve fund is about, or they’re not prioritizing it, when they look at all the needs of the state,” Stefanics says.

Stefanics says the reserve “has never been fully appropriated.” Legislators have funded it inconsistently since its creation in 2005, some years allocating zero appropriations. The state clawed back funds three times, and according to a recent analysis by Think New Mexico, by the end of 2022 (prior to this year’s appropriation) the reserve had just $300,000 in available funds.

The term of the state’s lease with the Jicarilla Apache Nation spans 10 years but so far is only funded for one year. Celene Hawkins, Colorado River Tribal Partnerships Program Director for the Nature Conservancy, says they will continue to support fundraising “through the life of this agreement.” The 2023 appropriation only applies to the current year, which means Riseley-White will return to the Legislature next year for funding to keep supplementing the San Juan’s flows.

Since hopes for a good monsoon evaporated under the summer’s relentless heat, the river’s spring infusion of water may prove even more critical.

“The future of water in New Mexico is just less water,” Oglesby says. “A lot less water.” That future includes hotter temperatures, which New Mexicans have felt acutely this summer. “That’s going to impact our watersheds and our fire regimes and our ability to maintain any kind of instream flows” to support rivers, “let alone water deliveries,” to farmers and cities, he says.

Tribes must be included in the state’s conversations about water, Vigil says, not least because the Jicarilla Apache Nation and the Navajo Nation are two of the largest water rights holders. But their contributions go beyond the material. “We can add some of these nuances,” he says, “in terms of the spiritual aspect of how we think about water.”

Plus, the state can’t solve its water conflicts on its own, Vigil says. “It’s going to take the state sovereigns to be involved in it, and in a partnership role.” The question, Vigil says, is, “How are we going to collectively build this water future together?”