Hurricane Helene and Subsequent Cleanup Efforts Have Decimated North America’s Most Biodiverse Waters – Inside Climate News

In Knoxville, Tennessee, there’s a minuscule warehouse tucked off the side of the road. Its tiny gravel parking lot is full. In the back of the cramped, wood-paneled building are dozens of aquarium tanks filled with endangered, threatened, imperiled, and at-risk fish species. 

This is Conservation Fisheries Incorporated (CFI), a nonprofit dedicated to preserving Appalachian freshwater diversity. It began as a graduate school project in the 1980s and has grown into a conservation powerhouse. 

One of the threatened species that CFI works with is the eastern hellbender, colloquially called the “snot otter,” which resides across Appalachia and the Midwest. Hellbenders have been at risk for decades, and were proposed for addition to the federal endangered list in 2024. Sedimentation, pollution and habitat disruption are some of the greatest threats to eastern hellbenders—and 2024’s Hurricane Helene exacerbated all of those issues. 

In 2025, after the catastrophic damages of the hurricane, Southern Appalachian rivers were deemed the third most endangered waterways in America. Researchers said many of the creatures in and around those waterways—with territories stretching into the Midwest and Southwest—are threatened, endangered or imperiled.

This is a gigantic area. The streams and rivers of Appalachia span around 400,000 miles. In the Southeastern region of Appalachia, these are North America’s most biodiverse freshwaters, housing 300 species of fish not found anywhere else—and more species of salamander than anywhere else in the world.

Eastern hellbenders reside beneath flat “shelter rocks”; according to Bo Baxter, director—and electrician, plumber, accountant, and whatever-else-needs-to-get-done—at CFI, Helene’s historic flooding scoured many areas of streams and rivers down to bedrock and deposited massive amounts of sediment and wreckage into others, disrupting these habitats. And during Helene, anything that was beside the rivers—or even near them—ended up in the water. Propane tanks, toxic chemicals and entire septic systems washed into Appalachia’s freshwater. 

For hellbenders, which breathe through their skin, Baxter says this is a major issue; any chemicals in the water will be in direct contact with highly sensitive salamanders. Similarly, yellowfin madtom, a threatened species of miniature catfish, don’t have scales, making them highly vulnerable to environmental toxins. 

Some of CFI’s members have madtoms tattooed on them, from a fundraising event between Conservation Fisheries and local tattoo artists. The founder of CFI is still there and still working; as he loads up his truck with gear to drive up to the streams, he jokes with the heavily pierced and tattooed 20somethings he’s hired, showing off his one, bright fish tattoo. 

After a conservation panel at the local queer coffee shop, conservationists of all ages huddle in a small cedar shed to socialize and share a few beers while a summer thunderstorm rages outside. Despite the storm and the constant political battles causing setbacks to environmental protections, the local community is relentless in their dedication to this work and their preservation of these species. 

“Helene was a 5,000-year flood,” Baxter said. “And these species have been swimming and crawling around in Appalachian waterways for millions of years. They’ve seen this before. But humans weren’t involved last time.” 

Dams impact the sedimentation process, gas stations leech toxins, and the post-hurricane cleanup process, such as debris cleanup and construction, poses an existential threat to Appalachia’s over 100 threatened and endangered aquatic species.

The federally endangered Appalachian elktoe mussel, for example, is dependent on stable habitats rich with gravel, sand and rock substrate. As a filter feeder, the elktoe is sensitive to pollutants and its presence is vital for maintaining the water quality that other endangered aquatic species also rely on. The floodwaters of Helene uprooted many of these mussels and washed their once sediment-rich habitats clean. 

The spotfin chub, a beautiful teal minnow and one of the first threatened species that Conservation Fisheries worked with, was already at risk from pollution and sedimentation before Helene. It used to be found in waterways from Virginia to Alabama; now it’s only found in the Little River, Buffalo and Emory Rivers, and Holston Rivers, in Tennessee, Virginia and North Carolina. 

Helene was so powerful, it moved house-sized boulders downstream, according to Erin Singer McCombs, Southeast conservation director at the nonprofit American Rivers. Now, she says, everything on the river banks looks like it’s been pressure washed. “It created a fresh, clean surface. It’s pretty stark. Everything is just so bright.” 

According to Baxter, this constitutes geological-scale change to these habitats and the species that live there. 

Full Effects Of Helene Remain Unknown 

For a few months after Helene, state agencies issued water contact advisories due to toxic pollution and dangerous debris. Biologists and conservationists couldn’t get into the water. 

According to Gary Peeples, field office supervisor at the Asheville Ecological Services Field Office of the U.S. Fish & Wildlife Service, many areas home to threatened and endangered species, both aquatic and land-based, still aren’t accessible. 

Because of this, biologists haven’t been able to conduct the kind of studies or surveys needed to fully understand how endangered, threatened and imperiled species have been affected. They’ve been forced to rely on anecdotal evidence, such as individuals reporting washed up, dead or injured hellbenders, even in some peoples’ basements. 

What is known is that the effects of Helene varied dramatically from place to place; while some areas were ravaged, others emerged with limited damage.

“It’s a very dramatic sight to behold,” Peeples said. “From a conservation standpoint, it points to the importance of having multiple protected populations scattered across a wide range so that if something does happen in one part, the species can still persist in another.” 

Storm Recovery Is Causing Its Own Type Of Damage

Many habitats destroyed by the flood will regenerate on their own, but over tens or maybe even hundreds of years in some places. 

What compounds a species’ ability to withstand the long process of regeneration is human presence. Reservoirs and dams, for example, create large sediment traps, leaving the areas downstream sediment-starved for far longer than is natural. 

And storm recovery efforts are continuing to impact habitats. After the storm, CSX, a private rail company, immediately began trying to recover a portion of railroad that had washed into the Nolichucky River in Irwin, Tennessee. They started mining the riverbed for ballast, using cheap, quick methods that would both disrupt the rapids on which the local tourism economy depends and create greater flooding risks for communities downstream. This area is one of the few habitats of the elktoe mussel and home to a “wild and scenic” gorge that protects imperiled species and helps support the $3.8 billion recreation industry of the French Broad River Basin in North Carolina and Tennessee. 

American Rivers, in conjunction with American Whitewater, had to sue three federal agencies—the U.S. Fish & Wildlife Service, the U.S. Forest Service, and the U.S. Army Corps of Engineers—to halt CSX’s actions. The Army Corps sent a letter prohibiting CSX from “any excavation or dredging of material from the Nolichucky River or its tributaries in both Tennessee and North Carolina” around two months after recovery efforts began. 

Gorge areas like these, Peeples said, were especially severely affected because the extreme amount of floodwaters didn’t have anywhere to go. While riverbanks could overflow, excess water in narrow canals had only one option: to move at rapid speeds. 

Cleanup from Helene is being led on a largely county-by-county basis, with work doled out to contractors. In areas where the Army Corps of Engineers led the cleanup, contractors were often paid by the ton of debris removed rather than by the linear foot of stream cleaned, according to McCombs. As a result, entire live trees, river snags, and more were being unnecessarily cut and removed, she said, resulting in denuded banks at greater risk for sediment erosion. 

The Army Corps of Engineers did not respond to requests for comment on the cleanup work.

The Little River previously had the region’s strongest population of Appalachian elktoe. After storm cleanup, McCombs recalls seeing only broken shells. 

Looking Forward

A new budget proposal by the Trump administration aims to slash funding for section six grants from the U.S. Fish & Wildlife Service and state wildlife entities. Section six, part of the Endangered Species Act, is what allows NGOs and nonprofits like Conservation Fisheries to work in conjunction with federal agencies. 

And it’s those agencies that took actions before Helene—ultimately saving lives—and are now educating others on how to be prepared for the next storm. 

For example, in 2021 and 2024, respectively, American Rivers worked to remove the Ward Mill dam and the Shulls Mill dam from the Watauga River. When Helene came, aging dams and their risk of failure caused major issues. The absence of the two dams saved lives and preserved critical infrastructure; where the dams had previously been, the river was able to flood and recede naturally. Now, the sedimentation cycle will also go unperturbed, allowing for quicker recovery.

As part of their work in preparation for these dam removals, American Rivers also conducted extensive biological monitoring, particularly of imperiled species such as the eastern hellbender. They were able to move hellbenders from the Shulls Mill site to the Ward Mill site, where there was perfect hellbender habitat but no population of hellbenders. 

To further prepare, McCombs believes more funds should be allocated for projects like dam removal and biological monitoring—and for studying Helene’s effects. 

“Right now we are in the process of doing the biological surveys post-Helene,” McCombs said. “We are finding hellbenders, which is really exciting.”