When Teresa Wicks surveyed the wetlands at the Lower Klamath National Wildlife Refuge in Siskiyou County, California, early this summer, they were alive with birds.
She saw black-necked stilts, avocets, and thousands of white-faced ibises. A single colony of eared grebes had about 1,500 nests. Birds and ducklings seemed to be everywhere.
“l don't think I've ever seen that many ducklings in one spot as I did at Lower Klamath [that day],” said Wicks, Eastern Oregon biologist and program manager at the Bird Alliance of Oregon.
The abundance made what happened next especially painful.
As drought tightened its grip on the Klamath basin, wetlands at Lower Klamath and the neighboring Tule Lake National Wildlife Refuge began drying rapidly. Many grebe nests were abandoned. Then avian botulism began killing waterbirds and hatchlings.
“Some of the birds that were sick and dying were ducklings and one- or two-day-old grebelings,” Wicks said. “That was particularly heart-wrenching.”
The outbreak threatened what had otherwise been an exceptional year for birds at the refuges, with an estimated 100,000 hatchlings and as many as 300,000 molting adults.
But as the outbreak worsened, groups often divided over the Klamath Basin's scarce water began working together to get more water to the refuges. Water users, irrigation districts, conservation groups, tribes and government agencies helped make the deliveries possible. Since the water arrived in mid-August, bird deaths have declined. Now, some of those groups are asking whether the emergency collaboration can yield something more permanent.
Their focus is a proposal known as “flow-through,” which would use the refuge wetlands to clean water from Upper Klamath Lake before returning it to the Klamath River.
But the proposal also illustrates the fundamental difficulty of managing water in the Klamath Basin: Helping one part of the ecosystem cannot come at the expense of endangered fish, tribal rights or other legal obligations.
Responding to the outbreak
Avian botulism, a natural part of Western ecosystems, is caused by bacteria that thrive in warm, stagnant water. As bird deaths mounted this summer, refuge staff began picking up diseased carcasses to prevent them from infecting other birds. Volunteers with Bird Ally X began treating sickened birds at a duck hospital.
The Klamath Water Users Association and irrigation districts worked with the Bureau of Reclamation to move more water into refuges. Adding water to these areas can cover exposed mudflats and improve circulation, making conditions less favorable for botulism.
“You need to be able to oxygenate that water by circulating it,” said Jeff McCreary, director of operations at Ducks Unlimited. “And if you can cool it down, that's even better.”
Under the federal operating schedule, the minimum required level for Upper Klamath Lake changed on Aug. 16, freeing some water for the refuges. Reclamation began sending more water to Tule Lake and Lower Klamath National Wildlife Refuges.
Since then, the number of dying birds has dropped. Wicks said the duck hospital is receiving fewer sick birds, and refuge staff are picking up fewer carcasses.
The U.S. Fish and Wildlife Service estimates that nearly 14,000 birds have died in this year’s botulism outbreak. That’s more than last year, when an estimated 3,400 birds died, but far fewer than 2024, when at least 128,000 birds perished.
In a news release, Reclamation credited the “hard work of the entire Klamath Basin community” for making these critical water deliveries possible.
The question now is whether that cooperation can extend beyond the immediate crisis.
Emulating an ecosystem
From the top of Sheepy Ridge, you can see the Tule Lake Wildlife Refuge to the east and Lower Klamath Wildlife Refuge to the west. The wetlands are bordered by a checkerboard of irrigated fields, some tawny under the late-summer sun.
“2026 is just a bugger of a year for everybody,” said Scott Seus, a third-generation farmer and president of Klamath Water Users Association. “Everybody's dealing with minimal inflows into whatever body of water you're talking about, whether it's the Klamath River or the reservoirs or the lake.”
Seus has brought dozens of people to this high point on Sheepy Ridge to help them see how the wetlands and agricultural lands fit into the larger watershed.
He advocates for flow-through, which would route water from Upper Klamath Lake through agricultural lands and refuge wetlands before returning it to the Klamath River. Existing pumps and a tunnel beneath Sheepy Ridge would help move the water between the refuges and complete the circuit.
Supporters say the approach could improve water circulation and quality while recreating some of the connections among lakes, wetlands and the river that existed before miles of canals, pumps, and other irrigation infrastructure transformed the Klamath Basin.
The wetlands are central to the idea. Sues calls them the system’s "filter."
“This is where you're going to take the high phosphorus that's coming out of Upper Klamath Lake,” he says.
Talks about flow-through ramped up this spring. As the botulism crisis worsened, conservation groups, the Karuk Tribe, water users, and local lawmakers urged Reclamation to put the idea into practice.
But it’s not so simple. Any movement of water must honor water rights and comply with federal protections for threatened coho salmon and endangered c’waam and koptu, two sucker fish species that dwell in Upper Klamath Lake and its tributaries.
“That is the hard part,” McCreary said. “How do we find a creative solution in which we can do this and not damage endangered species and not damage or infringe upon water rights?”
Not just birds
For the Klamath Tribes, any long-term solution must also protect c’waam and koptu.
The Klamath Tribes hold senior water rights that help maintain minimum levels at Upper Klamath Lake to protect fish spawning and nursery habitat. Those requirements can limit how much water is available to move elsewhere in the basin.
In a statement, the Klamath Tribes expressed support for the birds and long-term ecosystem-based strategies, while stressing that any solution should not come at the expense of c’waam and koptu, which are important to the Klamath Tribes’ culture and health.
Both U.S. Fish and Wildlife and the Klamath Tribes operate nurseries to raise the endangered suckers. But few young fish in Upper Klamath Lake are surviving to adulthood.
Seus points to a contrast downstream: He said suckers are thriving in the Lower Klamath refuge wetlands, even during drought years. He believes those wetlands could potentially serve as nurseries for c’waam and koptu.
Brad Parrish, water specialist for the Klamath Tribes, said fish raised outside the tribes’ treaty boundary cannot replace the populations they are trying to restore there.
“It does us no good as a tribe,” he said.
The goal, he said, is to restore c’waam and koptu to the point that tribal members can once again harvest them.
Poor water quality is one of several factors that impair c’waam and koptu. Parrish said restoring wetlands and streams around the Upper Basin could improve water quality and allow the lands to hold more water.
That, in turn, could give water managers more flexibility across the watershed.
“It’s resiliency associated with the functioning ecosystem,” says Parrish. “It's likely going to be different than what it was historically, but I think we could do better. There's a lot of work to do.”
The Klamath Tribes are collaborating on several projects, including the massive wetlands restoration project at Agency Lake, the uppermost arm of Upper Klamath Lake. Parrish said $3.17 million in federal funding for the restoration work remains on hold, slowing some of the work.
Moving past crisis
For now, the water entering the refuges is not part of a flow-through operation because it is not circulating back to the Klamath River.
Bird advocates hope the water will keep flowing until rain returns and temperatures cool. They also hope a flow-through pilot project can begin this fall.
For Wicks, the stakes are clear after the enormous bird losses of 2024 and another outbreak this year.
“These populations won't sustain losing over a hundred thousand birds every few years from botulism,” Wicks said. “We've got to make these long-term solutions happen and make them stick.”
Meetings between the different groups are still happening, even during a drought year when water is in short supply and as the tribes and water users continue to litigate over water deliveries.
Seus hopes that flow-through can eventually become part of Reclamation’s regular operating plan for the Klamath Project.
“I think that people believe in the concept,” Seus said. “Everybody's just got to let go of the devil they know and take a chance on the one they don't.”
