Botulism Returns to Tule Lake as Lower Klamath Wetlands Dry
Thousands of birds have died as conservation groups seek emergency water, local leaders back a flow through pilot, and the Klamath Tribes warn against shifting the crisis to endangered fish.
Klamath Refuges: The Klamath Basin National Wildlife Refuge Complex spans Southern Oregon and Northern California, including Lower Klamath and Tule Lake national wildlife refuges near the state line. Map by Winston Szeto, OPB. Source: U.S. Fish and Wildlife Service.
At A GLANCE
Current impact
Thousands of migratory birds have died at Tule Lake National Wildlife Refuge, with wildlife managers estimating about 150 deaths each day.
Growing danger
Lower Klamath National Wildlife Refuge is rapidly drying as warm, shallow, and stagnant water increases the risk of avian botulism.
Emergency request
Bird Alliance of Oregon is seeking 15,000 acre feet of water for Tule Lake and another 5,000 to 10,000 acre feet for Lower Klamath.
Proposed response
The Klamath Water Users Association is promoting a flow through pilot that would move water through farms and refuge wetlands before returning it to the Klamath River.
Tribal concern
The Klamath Tribes warn that lowering Upper Klamath Lake could increase risks to critically endangered c’waam and koptu protected by Treaty rights.
Why it matters
An estimated 100,000 to 150,000 birds died during the 2024 outbreak. Early water management helped sharply reduce bird deaths when botulism began returning in 2025.
KLAMATH FALLS, Ore. — Thousands of migratory birds have died this summer at Tule Lake National Wildlife Refuge, where wildlife managers estimate about 150 birds are now dying each day as another avian botulism outbreak spreads through warm, stagnant wetlands.
Lower Klamath National Wildlife Refuge faces the same growing threat as its wetlands rapidly dry. Conservation groups warn that young birds, molting waterfowl, and migrating birds could become trapped in shrinking areas of shallow water as summer temperatures remain high.
The outbreak at Tule Lake was first detected in early July, according to Bird Alliance of Oregon. The organization said conditions could become especially dangerous as more migratory birds arrive and many waterfowl enter a flightless molting period.
The renewed crisis comes just two years after the largest recorded bird die off at the Klamath Basin refuges. An estimated 100,000 to 150,000 birds died during the 2024 outbreak, with Bird Alliance citing an estimate of 140,000. An earlier outbreak in 2020 killed about 60,000 birds.
A Productive Year Turns Deadly
The danger follows what Bird Alliance described as a highly productive nesting season at Tule Lake and Lower Klamath.
The organization estimates the two refuges produced about 100,000 ducklings this year, along with more than 10,000 white faced ibis and hundreds of black necked stilt and American avocet chicks.
2024 Outbreak / Cover Photo: Dead waterfowl collected at Tule Lake National Wildlife Refuge during the 2024 avian botulism outbreak, which killed an estimated 100,000 to 150,000 birds. Moss Driscoll, Klamath Water Users Association.
Those numbers make the developing outbreak especially concerning. Young birds may be less able to leave deteriorating wetlands, while molting adults can temporarily lose their ability to fly.
Avian botulism develops when warm, shallow, poorly circulated water creates favorable conditions for toxin producing bacteria. Birds can ingest the toxin through aquatic insects and other invertebrates. When infected birds die, their carcasses can feed another generation of insects, continuing a cycle that can spread rapidly through crowded wetlands.
Botulism Toll: A dead waterfowl lies in shallow, algae covered water at Tule Lake National Wildlife Refuge during the 2024 avian botulism outbreak. Theresa Wick, Bird Alliance of Oregon courtesy of Klamath Water Users Association.
Carcass collection can slow that cycle, but the scale of previous outbreaks has overwhelmed response crews. At the height of the 2024 event, workers were collecting as many as 1,000 affected birds per day.
The difference between a manageable outbreak and a mass mortality event can come down to water movement.
Refuge managers saw the value of early action in 2025, when falling water levels brought the first signs that botulism could return. Refuge staff alerted the Tulelake Irrigation District and Bureau of Reclamation, and water operations were adjusted to improve conditions at Tule Lake.
The response made a dramatic difference. Ducks Unlimited reported that bird deaths fell from 100 to 200 per day to just one or two. Weekly totals dropped to between 10 and 20 birds, and water levels had stabilized by the beginning of fall migration.
Conservation Groups Seek Emergency Water
Bird Alliance is asking the Bureau of Reclamation and the Department of the Interior to provide 15,000 acre feet of water to Tule Lake as quickly as possible.
An acre foot is enough water to cover one acre one foot deep.
How much is 15,000 acre feet?
The requested amount equals nearly 4.9 billion gallons, enough to cover the entire surface of Crater Lake with almost 14 inches of water.
Spread across Upper Klamath Lake’s roughly 64,000 acre surface, that volume would equal about 2.8 inches of water. The actual effect would depend on inflows, releases, lake elevation, and the source of the delivery.
The organization wants the water used to fill Sump 1A and Sump 1B and begin moving water through the refuge. It is also seeking between 5,000 and 10,000 acre feet for Lower Klamath to slow the loss of wetland habitat there.
The request is intended as an immediate response to the disease threat, but it enters one of the most complicated water management systems in the West.
Water held in Upper Klamath Lake supports federally protected c’waam and koptu, also known as Lost River and shortnose suckers. Klamath River flows are managed for threatened coho salmon. Farms, ranches, communities, and wildlife refuges also depend on the same limited system.
Klamath Project irrigators are already operating with a 50 percent reduction in water deliveries this year, according to a joint commentary from elected officials representing Klamath, Modoc, and Siskiyou counties.
The county officials said the sacrifices already made across the Basin do not remove the need to respond to an immediate wildlife emergency. They called on federal agencies, Tribal governments, irrigation districts, conservation groups, and local governments to examine every lawful option for reducing bird deaths.
Wetland Habitat: Waterfowl take flight over restored wetland habitat at Lower Klamath National Wildlife Refuge. Chelsea Shearer.
Flow Through Proposal Gains Support
The county officials are backing a proposed Tule Lake Flow Through Pilot developed by the Klamath Water Users Association.
Rather than delivering water to one location and leaving it there, the proposal would move water continuously from Upper Klamath Lake through Klamath Project farmland, Tule Lake, and Lower Klamath before returning it to the Klamath River.
“Tulelake Flow Through represents a tangible opportunity to improve conditions across the Klamath Basin.”
Existing canals, drains, pumping plants, agricultural land, lakes, and refuge wetlands would be managed as parts of a connected system.
KWUA argues that moving water through the landscape could improve circulation in refuge wetlands, reduce botulism conditions, recharge shallow groundwater, support farms, and improve water quality before the water returns to the river.
The group also contends that improved circulation and expanded habitat could benefit salmon and endangered suckers. Those potential benefits would need to be evaluated through monitoring and additional scientific work.
In a July 10 article published by KWUA, Executive Director Elizabeth Nielsen said the Basin already has the infrastructure, expertise, and local commitment needed to put the Tule Lake Flow Through proposal into operation.
“Tulelake Flow Through represents a tangible opportunity to improve conditions across the Klamath Basin,” Nielsen said. “When we talk about the Basin, we’re talking about farms and ranches, fish, wildlife and refuges, the headwaters and the river, and the communities water supports. They’re all connected; they can all work together.”
Nielsen said growing participation from agencies, tribes, conservation organizations, and local stakeholders gives her hope that the Basin can move beyond repeated conflict and toward greater long term stability.
Connected Basin: Irrigated farmland and water delivery infrastructure within the Klamath Project, with Mount Shasta in the distance. The proposed flow through pilot would use the Basin’s existing canals, fields, wetlands, and pumping systems to move water through multiple uses before returning it to the Klamath River. Klamath Water Users Association.
In an August 3 commentary published by Capital Press, leaders from Klamath, Modoc, and Siskiyou counties described the Tule Lake Flow Through Pilot as a way to make available water serve several purposes before returning it to the Klamath River.
“The objective is straightforward: improve water circulation through refuge wetlands, reduce conditions that fuel botulism outbreaks, improve water quality, and gather scientific information to evaluate long-term ecological benefits throughout the Basin,” Tri-Counties said in the commentary.
They said the proposal is intended to remain within existing legal and regulatory requirements while preserving this year’s already reduced irrigation allocation. The county leaders also stressed that the pilot would not require anyone to surrender Treaty rights, weaken endangered species protections, or choose between fish and farms.
Klamath Tribes Warn Against Shifting the Risk
The Klamath Tribes responded to the growing refuge emergency by saying they are heartbroken by the loss of migratory birds and also want healthy wetlands, thriving wildlife, and a restored ecosystem.
The Tribes said the birds are important Treaty resources, but warned that the current crisis cannot be separated from decades of changes to the Basin’s natural water system.
“We wouldn’t have this issue if we had a functioning ecosystem,” Klamath Tribes Water Rights Specialist Brad Parrish said.
The Tribes’ concern is that emergency water for Tule Lake and Lower Klamath could come at the expense of c’waam and koptu in Upper Klamath Lake. The two critically endangered fish are central to Tribal culture, identity, and Treaty rights, and lake levels are managed under legal requirements intended to prevent their extinction.
Treaty Resources: The Klamath Tribes say additional water deliveries to the refuges should not increase risks to endangered c’waam and koptu in Upper Klamath Lake, which remain central to Tribal culture, identity, and Treaty rights. Jason Ching, U.S. Geological Survey.
According to the Tribes, water quality in Upper Klamath Lake continues to decline, placing the fish under additional stress. Lowering the lake further to supply the refuges could increase that danger.
Chairman William E. Ray Jr. placed the dispute within the Treaty of 1864. He said the Tribes’ protected resources include water, fisheries, subsistence and medicinal plants, big game, and other living resources that have sustained Tribal people for generations.
“Addressing one ecological crisis by increasing the risk to another is not responsible stewardship”
Ray said the Tribes should not be asked to sacrifice those resources because of conditions created by earlier changes to the Basin. He also said they should not be blamed for exercising their sovereignty to protect them.
The Tribes said protecting birds and protecting fish should not be treated as competing goals. They called for collaborative, science based restoration that improves the health of the entire Basin while honoring Tribal sovereignty, Treaty rights, existing law, and the best available science.
A Familiar Crisis With Little Time
The Klamath Basin has seen this pattern before. An outbreak in 2020 killed more than 60,000 birds. In 2024, water levels dropped after a productive nesting season, and the disease spread through Tule Lake as birds crowded into shrinking wetlands. An estimated 100,000-150,000 birds died, making it the largest recorded outbreak at the Klamath refuges.
This summer, the disease has returned as Lower Klamath dries and conditions at Tule Lake again become warm, shallow, and stagnant. Thousands of birds have already died, and more are expected to arrive as fall migration builds.
The most dangerous part of the season may still be ahead. Without improved water circulation or another change in conditions, wildlife managers and conservation groups warn that the outbreak could accelerate as more birds gather in the remaining wetlands.
What Comes Next?
The immediate question is whether federal officials will provide additional water or approve some version of the Tule Lake Flow Through Pilot soon enough to change conditions before the outbreak reaches its seasonal peak and more migrating birds arrive.
The larger question is whether the Klamath Basin can move beyond emergency responses and develop a system that keeps the refuges functioning without increasing the danger to c’waam, koptu, Klamath River fish, farms, or Tribal Treaty resources.
The last two summers demonstrate how much can depend on timing. In 2024, delayed and insufficient water movement was followed by a record outbreak that killed more than 100,000 birds. In 2025, managers changed operations after the first warning signs appeared, and daily deaths dropped sharply. This year, thousands of birds have already died as refuge wetlands again become warm, shallow, and stagnant.
Jefferson Daily contacted the Bureau of Reclamation and Department of the Interior seeking information about the current outbreak, the emergency water request, and the proposed flow through pilot. Neither agency had provided a response or outlined its planned action by publication.
For the birds now concentrated at Tule Lake and the wetlands disappearing at Lower Klamath, the debate is no longer about preventing a future emergency. The emergency has already begun. What happens next will depend on whether water managers can improve conditions before the outbreak reaches its seasonal peak.
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