Klamath Refuges Hit with One-Two Punch: Botulism and Avian Influenza

by Bird Wicks, Eastern Oregon Biologist and Program Manager

This spring, highly pathogenic avian influenza (HPAI) arrived in the Klamath Basin. By June it had spread among the Eared Grebes of the Klamath National Wildlife Refuge Complex, killing hundreds of birds. In early August, as water levels declined and water became warm and stagnant, another disease emerged, killing hundreds of birds in the first few days. While the U.S. Fish and Wildlife Service (USFWS) has not received lab results, independent biologists witnessed birds displaying symptoms commonly associated with botulism. As of the printing of this issue of the Warbler, it’s estimated that 5,000 birds have died.

Dead bird floating in the water, due to botulism outbreak at Klamath

Unlike HPAI, botulism affects the nervous system, so sick birds appear unsteady on their feet and cannot fly or hold up their heads. This paralysis causes many infected waterfowl and waterbirds to drown. While birds with HPAI appear unwell, they do not appear to suffer from paralysis.

Botulism is a naturally occurring bacteria. However, large-scale die-offs of birds are not typically part of the botulism cycle. In Klamath, botulism outbreaks usually start in late summer, are short-lived, and kill only a few hundred birds. Yet as water scarcity has become the norm, outbreaks have increased in severity. The outbreak of 2020 killed 60,000 waterfowl, waterbirds, and shorebirds. Without intervention, this latest outbreak will likely see tens of thousands of dead birds. The Pacific Southwest Region of the USFWS and the Bureau of Reclamation claim that disease is a “normal part of the summer cycle.” But what we’re seeing in the Klamath Basin is far from normal.

Since time immemorial

Before colonization, the Klamath River and its watershed functioned synergistically, with the wetlands of the Klamath Basin acting as a sponge, soaking up water during wet periods and giving water to the river during drier periods. The verdant wetlands and lakes of the Klamath Basin supported endemic suckers like the short-nosed (koptu) and Lost River (c’waam), whose existence is closely tied to the Indigenous peoples of the Klamath Basin: the Klamath Tribes and the Modoc Nation. The wetlands allowed the Klamath River to carry abundant Chinook and coho salmon, whose existence is tied to the Indigenous peoples of the Klamath River: the Yurok, Karuk, Hoopa, and Shasta.

Klamath Basin wetlands and lakes also created ample habitat for migrating and breeding waterfowl, waterbirds, and shorebirds. Indeed, the Klamath Basin is one of the most important areas in the Pacific Flyway for water-associated bird species. The Indigenous stewards of the Klamath watershed have a deep understanding of how the natural hydrology functioned to create such a productive system. What happens to the wetlands happens to suckers, to salmon, to birds, and to the people indigenous to the basin.

Ripple effects

Klamath Basin wetlands and lakes drew settlers to the region. With the creation of the Bureau of Reclamation (BOR) in 1902, arid lands were targeted for flooding, and wetlands were targeted for draining. As the Klamath River Tribes were removed from their land, wetlands were drained and diked, canals were dug, and the river was turned into a series of reservoirs (though today, for the first time since the dams were built, the Klamath River is considered free-flowing as the dam removal project is progressing on schedule). In the 117 years since the Klamath Project was started, wetlands have become drier (and scarcer), Upper Klamath Lake water quality has become increasingly poor, and fish- and bird-killing diseases have become more common. Shallow warm water spawns botulism in wetlands and ich (white spot disease) in rivers, both of which have caused mass die-offs in birds and salmon respectively since 2000.

Wetland loss, changes to natural hydrology, and declining water quality have contributed to population declines in Lost River (c’waam) and short-nosed (koptu) suckers, and declines in Chinook and coho salmon along the Klamath River. As of 2023, Ducks Unlimited estimated a 25% decline in waterfowl numbers in the Pacific Flyway, while other flyways have relatively stable populations. It’s hard to ignore the impact of losing more than 90% of the wetlands in the most important stopover site in the Pacific Flyway. What happens in the Klamath Basin has ecological and social ripple effects.

A potential path forward

Bird Alliance of Oregon wrote to the BOR and demanded that they send adequate water to the refuges to avert a catastrophic die-off. Shortly after, we received notice that 5,000-10,000 acre feet of water was delivered to Tule Lake and Lower Klamath NWR on Saturday, August 17. Though the water is not enough in the long term, it should be enough to help the hundreds of young waterfowl and waterbirds hatched this year reach fledging. It will also help reduce the impacts of avian influenza and botulism.

Many players will have an important role in solving this crisis. The Oregon Water Resources Department has overappropriated water throughout the basin. USFWS refuge staff must watch year after year as water is delivered to agriculture before wildlife, even on the refuges and despite a legal ruling giving priority to refuge wetlands. Because the refuges have junior water rights for wildlife, they have no say over where water goes or when. That responsibility falls to BOR, which owns and operates the infrastructure that moves water throughout the Klamath Project.

Tribes, irrigators, USFWS staff, and other conservation groups have been working on possible solutions that promote wetlands on the refuge, improve water quality, and reconnect Lower Klamath to the Klamath River. These projects would, in essence, move water to Tule Lake and Lower Klamath, creating wetlands that water would flow through on its way back to the river, removing phosphorus, high nutrient loads, and generally cooling the water before it reenters the river. This would mimic natural hydrology, provide cleaner water for spawning salmon, provide refugia for growing suckers (who would then rejoin the Upper Basin population to spawn) and wetlands for birds, in theory without increasing water demands from Upper Klamath Lake. Creative, collaborative ideas such as these provide glimmers of hope for the future of the Klamath Basin and the wetlands, wildlife, and people who live there.