US Lakes Where Native Fish Are Disappearing Fastest

Native fish populations across the United States are disappearing from the lakes they have inhabited for thousands of years, driven by invasive species, habitat loss, pollution, and a warming climate. Several lakes stand out for the severity and pace of these declines. This is not a story about gradual change. In some of these lakes, native species that once numbered in the millions are now functionally gone. In others, the clock is ticking against a dwindling population. What is happening in these waters is a reflection of what many freshwater ecosystems are facing globally.

Lake Erie

At their peak, cisco, also called lake herring (Coregonus artedi), were so abundant in Lake Erie that this species supported the largest commercial freshwater fishery in the Great Lakes. That is not a small claim. The Great Lakes contain about 21 percent of the world's surface fresh water, and cisco was the engine of its most productive lake fishery.

However, the population collapsed in 1925, driven primarily by commercial overfishing, though habitat loss and eutrophication accelerated the decline through the mid-20th century. Eutrophication is the excessive enrichment of a body of water with nutrients, especially phosphorus and nitrogen. Today, cisco are considered almost entirely locally extinct from Lake Erie. Between 1995 and 2020, only 56 fish thought to be cisco were captured in commercial gillnets and trawls across the entire lake. An expert panel convened in 2024 by the Great Lakes Fishery Commission to assess the situation reached a stark conclusion. The panel determined that no visible cisco populations remain in Lake Erie.

Restoration efforts are now underway. In 2025, the New York State Department of Environmental Conservation and the U.S. Fish and Wildlife Service began a 10-year experimental reintroduction of cisco into the New York portion of Lake Erie. They have thus far stocked 90,000 yearlings offshore of Dunkirk, New York. Researchers will be tracking whether reintroduced fish can establish any foothold in a lake that has changed dramatically since cisco last thrived there.

Lake whitefish (Coregonus clupeaformis) are following a similar arc. They were once the most popular commercial species in Lake Erie. Between 1910 and the late 1940s, about two to seven million pounds of whitefish were commercially harvested from the lake annually. But overfishing led to a serious decline in their numbers by the 1950s. During the 2016 to 2020 reporting period published by the Great Lakes Fishery Commission, the average annual harvest was about 90,000 pounds.

The drivers behind the whitefish's current decline are still being studied, but a 2021 review by the Great Lakes Fishery Commission identified warming water temperatures and the loss of ice cover as primary factors. Ice protects whitefish embryos from winter wave action during a critical incubation period on shallow spawning shoals. Additionally, non-native dreissenid mussels became established in several of the Great Lakes in the early 1990s. Researchers believe the rise of these invasive mussels are also likely playing a role in the decline of the whitefish population, but exactly how this is happening is still being studied.

Flathead Lake

Bull trout (Salvelinus confuentus) numbered an estimated 20,000 adults in the broader Flathead Basin in the early 1950s. After Hungry Horse Dam blocked spawning routes in 1953, that figure dropped to around 13,000 by 1982. Today biologists estimate approximately 3,000 adult bull trout remain in the basin, while invasive lake trout in Flathead Lake number over one million.

Beginning in 1905, state fisheries managers introduced nonnative species to boost recreational fishing. Today more than 20 fish species inhabit the lake, but invasive lake trout, lake whitefish, and Mysis shrimp dominate the food web. A 2021 study from the University of Montana's Flathead Lake Biological Station and USGS documented how these introduced species now sit at the top. The shrimp outcompeted the kokanee for zooplankton, collapsing that population entirely by the 1990s. In turn, the shrimp population boomed and invasive lake trout fed heavily on them, significantly increasing their own population. As they grew larger in both size and population, the lake trout targeted the native bull trout as prey. Additionally, invasive lake trout force native fish into suboptimal habitats where they feed on less nutritious food sources, weakening populations over generations until they cannot sustain themselves. Research published in Science Advances found bull trout occupancy across Montana declined 18 percent between 1993 and 2018 and is predicted to fall another 39 percent by 2080.

The southern half of Flathead Lake sits on the Flathead Reservation, home to the Confederated Salish and Kootenai Tribes, for whom bull trout are culturally significant and have been a winter food staple for generations. To combat their population decline, the Confederated Salish and Kootenai Tribes launched a two-pronged effort to reduce the invasive lake trout population. Through community fishing events and a commercial netting operation established in 2017 called Native Fish Keepers, Inc., they remove about 80,000 invasive lake trout per year.

Pyramid Lake

The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) and cui-ui once thrived in Pyramid Lake, Nevada, but a dam built over 100 years ago has sent their population numbers plummeting.

The Derby Dam was completed in 1905 and diverted half of all Truckee River water to agricultural fields near Fallon, greatly destabilizing the lake and its inhabitants. By 1967, Pyramid Lake had dropped by an estimated 80 feet. Access to spawning grounds in the Truckee River was blocked by the dam, making the Lahontan cutthroat trout functionally extinct from Pyramid Lake by the 1940s. The cui-ui, a sucker fish found nowhere else on Earth, was expected to follow.

A fishery scientist eventually identified a remnant population of the Lahontan cutthroat trout surviving in a creek on the Nevada-Utah border. The remarkable find allowed the Pyramid Lake Paiute Tribe to propagate the trout and successfully reintroduced it into the lake. But the recovery has required sustained, decades-long effort. The tribe manages a fish hatchery where the trout are spawned and raised as juveniles until they can be released into the lake. Because Lahontan cutthroat trout are obligate freshwater spawners, their eggs cannot survive in Pyramid Lake's raised salt concentration. Despite this work, a US Fish and Wildlife Service status report determined that only five of 71 populations of Lahontan cutthroat trout are considered resilient, and less than half are likely to be resilient into the future. Less than 0.4 percent of lake-dwelling trout are self-sustaining without hatchery supplementation.

The cui-ui faces a parallel crisis. Tribal members stopped catching them in the 1980s as the population plummeted, representing a significant cultural loss. The Pyramid Lake Paiute Tribe refers to themselves as Cui-ui Tucutta in their indigenous language, meaning "the Cui-ui eaters." Their drastic decline was caused in large part because of the Numana Dam, an irrigation diversion structure built in 1917. It has functioned as a barrier to migration for both the endangered cui-ui and the threatened Lahontan cutthroat trout.

Recovery efforts have accelerated in recent years. The tribe received $8.3 million from the Bipartisan Infrastructure Law to modify Numana Dam, with funds used to build a large underwater ramp stretching from bank to bank. This modification allows fish to swim up and over the structure, reopening 65 miles of river for spawning migration. The ramp is designed specifically for the cui-ui's swimming capacity and speed, and is expected to allow up to 600,000 cui-ui to access new spawning grounds.

Upper Klamath Lake

Upper Klamath Lake in southern Oregon holds two fish found nowhere else on Earth: the Lost River sucker (Deltistes luxatus), known to the Klamath Tribes as c'waam, and the shortnose sucker (Chasmistes brevirostris), or koptu. Both were listed as endangered in 1988. Their combined adult population has declined roughly 87 percent between 2001 and 2023.

The crisis is not adult mortality, but the failure of young fish to survive in enough numbers to replace them. The fish alive today are an aging population with almost nothing behind them. A century of agricultural land use upstream has loaded the lake with excess phosphorus, fueling massive cyanobacteria blooms each summer. Near-anoxic (without oxygen) conditions produced during the dying off process of the blooms are strongly implicated in mass juvenile mortality. The US Fish and Wildlife Service has released over 35,000 juvenile suckers into the lake since 2018, but fewer than one percent of tagged fish have been detected surviving.

Klamath Tribes are continuing to push for the land use and water quality reforms that biologists increasingly agree are the only path to real recovery. Roughly 95 percent of the wetlands that once ringed Upper Klamath Lake are gone from over a century of excess phosphorus levels due to industrial agricultural activity. Those wetlands historically provided protected habitat for juvenile Lost River and shortnose suckers to reach maturity before venturing into the lake, where predators are plentiful. Most consequentially, the Army Corps of Engineers in the 1950s straightened and diked the Sprague River, turning it into a conduit that scoured naturally occurring phosphorus from soils and routed it directly into the lake.

In January 2025, a levee was breached, reconnecting roughly 14,000 acres of former wetlands to Upper Klamath Lake, a project led by the Klamath Tribes in conjunction with the US Fish and Wildlife Service. This reconnection of wetland habitats to Upper Klamath Lake may significantly increase the chance of recovery for the lake's native suckers.

A Pattern Larger Than Any One Lake

These lakes are separated by hundreds of miles, but the arc of each native fish's decline follows a recognizable pattern. Native fish once thriving in a balanced ecosystem have been reduced to remnant populations from over a century of overfishing, habitat loss and destruction, the introduction of invasive species, and pollution. In each case, recovery efforts are underway, often led in large part by the indigenous tribes who have kept a cultural connection to these species for generations. Reintroduction programs, dam modifications, wetland restoration, prioritizing indigenous stewardship, and invasive species removal are helping to turn the tide. Whether these efforts have arrived in time, and whether they can succeed against the larger effects of climate change is still an open question.