In 2025, after the catastrophic damages of the hurricane<\/a>, Southern Appalachian rivers were deemed the third most endangered waterways<\/a> in America. Researchers said many of the creatures in and around those waterways\u2014with territories stretching into the Midwest and Southwest\u2014are threatened, endangered or imperiled.<\/p>\n This is a gigantic area. The streams and rivers of Appalachia span around 400,000 miles<\/a>. In the Southeastern region of Appalachia, these are North America\u2019s most biodiverse freshwaters<\/a>, housing 300 species of fish not found anywhere else\u2014and more species of salamander than anywhere else in the world.<\/p>\n Eastern hellbenders reside beneath flat \u201cshelter rocks\u201d; according to Bo Baxter, director\u2014and electrician, plumber, accountant, and whatever-else-needs-to-get-done\u2014at CFI, Helene\u2019s historic flooding<\/a> 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\u2014or even near them\u2014ended up in the water. Propane tanks, toxic chemicals and entire septic systems washed into Appalachia\u2019s freshwater<\/a>.\u00a0<\/p>\n For hellbenders, which breathe through their skin<\/a>, 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\u2019t have scales, making them highly vulnerable to environmental toxins.\u00a0<\/p>\n Some of CFI\u2019s members have madtoms tattooed on them, from a fundraising event between Conservation Fisheries and local tattoo artists<\/a>. 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\u2019s hired, showing off his one, bright fish tattoo.\u00a0<\/p>\n 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<\/a> and the constant political battles causing setbacks to environmental protections<\/a>, the local community is relentless in their dedication to this work and their preservation of these species.\u00a0<\/p>\n \u201cHelene was a 5,000-year flood,\u201d Baxter said. \u201cAnd these species have been swimming and crawling around in Appalachian waterways for millions of years. They\u2019ve seen this before. But humans weren\u2019t involved last time.\u201d\u00a0<\/p>\n 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\u2019s over 100 threatened and endangered aquatic species<\/a>.<\/p>\n 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.\u00a0<\/p>\n The spotfin chub, a beautiful teal minnow and one of the first threatened species<\/a> 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\u2019s only found in the Little River, Buffalo and Emory Rivers, and Holston Rivers, in Tennessee, Virginia and North Carolina.\u00a0<\/p>\n 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\u2019s been pressure washed. \u201cIt created a fresh, clean surface. It\u2019s pretty stark. Everything is just so bright.\u201d\u00a0<\/p>\n According to Baxter, this constitutes geological-scale change to these habitats and the species that live there.\u00a0<\/p>\n Full Effects Of Helene Remain Unknown\u00a0<\/p>\n For a few months after Helene, state agencies<\/a> issued water contact advisories due to toxic pollution and dangerous debris. Biologists and conservationists couldn\u2019t get into the water.\u00a0<\/p>\n 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\u2019t accessible.\u00a0<\/p>\n Because of this, biologists haven\u2019t been able to conduct the kind of studies or surveys needed to fully understand how endangered, threatened and imperiled species have been affected. They\u2019ve been forced to rely on anecdotal evidence, such as individuals reporting washed up, dead or injured hellbenders, even in some peoples\u2019 basements.\u00a0<\/p>\n 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.<\/p>\n \u201cIt\u2019s a very dramatic sight to behold,\u201d Peeples said. \u201cFrom 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.\u201d\u00a0<\/p>\n Storm Recovery Is Causing Its Own Type Of Damage<\/p>\n Many habitats destroyed by the flood will regenerate on their own, but over tens or maybe even hundreds of years in some places.\u00a0<\/p>\n What compounds a species\u2019 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.\u00a0<\/p>\n This story is funded by readers like you.<\/p>\n Our nonprofit newsroom provides award-winning climate coverage free of charge and advertising. We rely on donations from readers like you to keep going. Please donate now to support our work.<\/p>\n Donate Now<\/a> <\/p>\n 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<\/a> and home to a \u201cwild and scenic\u201d 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.\u00a0<\/p>\n American Rivers, in conjunction with American Whitewater, had to sue three federal agencies\u2014the U.S. Fish & Wildlife Service, the U.S. Forest Service, and the U.S. Army Corps of Engineers\u2014to halt CSX\u2019s actions. The Army Corps sent a letter prohibiting CSX from \u201cany excavation or dredging of material from the Nolichucky River or its tributaries in both Tennessee and North Carolina<\/a>\u201d around two months after recovery efforts began.\u00a0<\/p>\n Gorge areas like these, Peeples said, were especially severely affected because the extreme amount of floodwaters didn\u2019t have anywhere to go. While riverbanks could overflow, excess water in narrow canals had only one option: to move at rapid speeds.\u00a0<\/p>\n 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.\u00a0<\/p>\n The Army Corps of Engineers did not respond to requests for comment on the cleanup work.<\/p>\n The Little River previously had the region\u2019s strongest population of Appalachian elktoe. After storm cleanup, McCombs recalls seeing only broken shells.\u00a0<\/p>\n Looking Forward<\/p>\n A new budget proposal by the Trump administration aims to slash funding<\/a> for section six grants from the U.S. Fish & Wildlife Service and state wildlife entities. Section six, part of the Endangered Species Act,<\/a> is what allows NGOs and nonprofits like Conservation Fisheries to work in conjunction with federal agencies.\u00a0<\/p>\n And it\u2019s those agencies that took actions before Helene\u2014ultimately saving lives\u2014and are now educating others on how to be prepared for the next storm.\u00a0<\/p>\n![\"A](\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/07\/DSCN1858-edit_-1024x683.jpg\"\/)
A Mountain Madtom (Noturus eleutherus). Credit: Derek Wheaton<\/p>\n![\"An](\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/07\/GettyImages-2176563550.jpg\"\/)
An aerial view of flood damage wrought by Hurricane Helene along the Swannanoa River on Oct. 3, 2024, in Asheville, N.C. There were 27 confirmed weather and climate disasters last year with losses exceeding $1 billion in the United States. Credit: Mario Tama\/Getty Images<\/p>\n