This May, while collecting live fish for their annual aquatic pathogen assessment on the Klamath River in Northern California, Yurok Tribe biologists made a shocking discovery: Over 70 percent of the young, ocean-bound Chinook salmon captured in their traps were dead. Almost all the fish tested upstream were infected with Ceratonova shasta, a parasite that relies on both fish and annelid worms as hosts. Barry McCovey, senior fisheries biologist for the Yurok Tribe, expects most of the infected fish to die.

“When something like this happens, it’s devastating in the moment because we’re seeing all these baby salmon die,” McCovey says. “But what’s even worse is we know we will feel it again in three years when these fish don’t return to the river to feed our people.”

Fall Chinook is the only commercial salmon run remaining in a river that was once the third-most-productive on the West Coast. Rates of C. shasta infection have soared in recent years, and the Yurok Tribe has not had a viable fishery since 2015. The parasite occurs naturally, but unnatural factors, including the presence of four hydroelectric dams on the main stem of the Klamath, encourage the disease. Drought years make the problem worse.

And 2021 promises to be one of the worst drought years on record. More than half of the western United States is currently experiencing extreme drought, according to the US Drought Monitor. This includes the vast Klamath watershed, which spans over 10 million acres in southern Oregon and Northern California. In the Klamath Basin, everyone is suffering—commercial fishermen; the Yurok, Karuk, and Hoopa Tribes downstream of the dams; farmers and ranchers in the upper basin; the thousands of birds that rely on water deliveries from the Klamath Project; and the upstream Klamath Tribes, which are doing everything they can to save the c’waam and koptu, two critically endangered species of suckerfish that inhabit Upper Klamath Lake in Oregon. 

In May, the Bureau of Reclamation canceled a “flushing flow” that would have helped out-migrating salmon and announced that, for the first time since 1907, the agency was shutting down the main canal in the vast Klamath Project, which provides irrigation water to about 240,000 acres of farmland near the Oregon-California border. The project also supplies water to a complex of wildlife refuges that support thousands of ducks, geese, and shorebirds that migrate along the Pacific Flyway. Last year, at least 60,000 birds died of avian botulism when shrunken wetlands forced them to crowd together.

The suffering isn’t new. A drought in 2001 prompted some farmers to defy federal managers and open the headgates to irrigation canals in protest. The following year, the Lower Klamath tribes—the Yurok, Karuk, and Hoopa—witnessed a devastating die-off of spawning adult Chinook, which was linked in part to low flows on the river. 

National headlines often frame the chronic water shortage in the Klamath Basin as “farmers versus fish.” The reality is far more complex—and worrisome. Since the 2002 fish kill, abnormally dry years have predominated in the Klamath Basin, including a prolonged drought that stretched from late 2011 to early 2017. 

McCovey says good water years are increasingly rare. “We’re thinking that this is the new normal, that we’ll be in a perpetual state of drought,” he says. “Things are changing really fast.”

The US Climate Normals, 30-year averages published by NOAA, show the Klamath Basin growing both warmer and dryer. A 2011 report from the Bureau of Reclamation predicts reduced snowpack, reduced run-off, and changes in the timing of run-off—all of which will make life even harder for the region’s farmers, fish, and Native American nations. 

“But the reality is even when there is water, we're not doing a good job of managing it in a way that stores it in healthy riparian wetland systems,” says Becky Hatfield-Hyde, a multi-generation rancher in the Upper Klamath Basin in Oregon.

Four hydroelectric dams artificially divide the Klamath watershed, cutting off anadromous fish from over 400 miles of upper basin habitat and fostering toxic algae blooms in the reservoirs behind them. Historic logging, fire suppression, and agriculture have greatly altered the landscape.

Upper Klamath Lake, where the Klamath River originates, is naturally shallow and high in nutrients, thanks to phosphorus-rich soils. But the lake’s vast fringe of filtering wetlands is largely gone, and the tributaries that feed it have been straightened to hasten water delivery. Today Upper Klamath Lake is “hyper-eutrophic”: An overabundance of nutrients feeds massive algae blooms that consume oxygen and make the lake inhospitable to many kinds of aquatic life. The poor water quality harms young c’waam and koptu. Even when the suckers do spawn successfully, not enough young are surviving to replace older generations.

The Klamath Tribes hold a conservation easement on one of Hatfield-Hyde’s properties, and she has worked with the tribe and several partners to narrow stream channels and improve riparian conditions while still actively ranching. “But the reality is the way I manage cattle on a river cannot change that bigger underlying complexity that came from straightening the Sprague River,” she says, referring to one of the lake’s tributaries.  

Nell Scott, Klamath restoration director for Trout Unlimited, works with ranchers in the upper basin on projects that protect and enhance habitat for fish and birds. This includes fencing streams, removing fish barriers, screening irrigation ditches, and reconnecting streams with their floodplains. Despite their benefits, Scott agrees “random acts of conservation” aren’t enough to improve water quality in the lake. 

“Getting these streamside floodplains connected and protected across the whole landscape would be one of the most important things we could do,” Hatfield-Hyde says, adding that such an endeavor would require funding and clear incentives for landowners. 

Scott, Hatfield-Hyde, and others bemoan the demise of the Klamath Basin Restoration Agreement. Hashed out among a diverse group of stakeholders, the agreement would have funded comprehensive restoration in the Klamath Basin and represented a compromise between irrigators and the tribes. Congress killed the plan in 2015 by refusing to vote on it.

Scott calls the death of the consensus agreement a “huge loss” for the Klamath Basin. “I think it would've made relations better. It would've made the ecosystem better.” 

Since 2013, the Klamath Tribes have exercised their senior water rights, and in drought years have chosen to keep water in-stream for the benefit of suckers, which the Klamath Tribes have long relied on for sustenance. For several years, this has curtailed irrigation to ranchers in the upper basin.

There is a real tension between farmers and fish, but the irrigators in the Klamath Project also direct water to the complex of wildlife refuges in the dry region straddling the Oregon-California border. When farmers get less water, so do the birds. Groups like California Waterfowl are working to secure a high-priority water right for the refuges.

Extreme drought years also pit the needs of salmon downstream of the dams against those of c’waam and koptu. The US Fish and Wildlife Service sometimes instructs the Bureau of Reclamation to release “flushing flows” at critical times to help young Coho salmon on their migration out to the sea. But the guidance document for c’waam and koptu mandates that levels in Upper Klamath Lake be maintained above a threshold to ensure successful spawning. This spring, the Klamath Tribes sued to force the bureau to maintain lake levels for the suckers. 

McCovey acknowledges the cultural and ecological significance of c’waam and koptu. At the same time, he says, the bureau’s mismanagement of water in 2020 is adding to this year’s crisis and that it is “absolutely imperative” that the agency maintain river flows to help salmon through the summer. “Otherwise, we risk unprecedented ecosystem collapse and the potential for an adult Chinook fish kill in the fall similar to the one in 2002.”

Farmers and ranchers who use irrigation water, the various upstream and downstream tribes, commercial fishing groups, and NGOs have all used litigation, mostly against the Bureau of Reclamation, to fight for the precious resource that will help fish, birds, and their families survive. 

“We want to find sustainable solutions for fish and for agriculture,” says Amy Cordalis, a fisherwoman and the Yurok Tribe’s general counsel. “We don't want to have to go through all this litigation, but we find ourselves in situations where there are no other options.” 

Tensions are rising with the temperatures. A protest encampment has sprung up on private land near the A Canal’s headgate in Klamath Falls, coordinated by a local chapter of People’s Rights Oregon—a group with ties to Ammon Bundy, who staged an armed takeover of the Malheur National Wildlife Refuge in 2016. The two farmers who organized the encampment have pledged to breach the headgate and attempt to release water in defiance of the bureau’s recent decision. Ammon Bundy himself has also promised to show up, if asked. The Klamath Water Users Association has urged for calm, careful to separate itself from the other group while acknowledging their right to protest. 

Meanwhile, the Bureau of Reclamation has authorized millions of dollars in relief, including $15 million for farmers and $3 million for area tribes. Oregon Senators Ron Wyden and Jeff Merkley, both Democrats, and Representative Cliff Bentz, a Republican, underscored the need for a unified response in a May 15 press release that called for additional federal resources for the parched region. And on May 18, Representatives Bentz and Doug LaMalfa, a California Republican, proposed a $57 million aid package for the Klamath Basin. While most of the aid would go to farmers, the package also includes $2.5 million for the Lower Klamath and Tule Lake refuges, food aid for tribes, and relief for commercial fishermen.

Although Hatfield-Hyde applauds these bipartisan efforts, she says a true solution will require getting past crisis thinking and “spitfire litigation.” “Let's stop throwing our money at crisis,” she says. “Let's throw our money at those long-term restoration goals.” 

The much-awaited decommissioning of the four Klamath dams, slated to begin in 2023, should bring some relief. Removal of the structures will improve water quality below the dams and open up new habitat to salmon above them. But dam removal alone will not stave off another crisis in the Klamath Basin.

The Yurok Tribe, which is engaged in extensive restoration on the Klamath and its tributary streams, is also calling for the creation of a “long-term stakeholder-driven plan” that takes climate change into account. 

“Everyone is feeling the pain right now,” Cordalis says. “One good thing about pain is it can be motivation to figure out how to take it away. I really hope we can use all the attention [that’s focused] on the Klamath right now to find a long-term sustainable solution.”

If it’s true that in crisis lies opportunity, this well may be the year that such an effort materializes. Otherwise, it is certain that the watershed will see more dead fish, dying birds, and suffering people in the years to come.