The Katiti Petermann Aboriginal Land Trust in central Australia contains significant biological and cultural assets including the World Heritage-listed Uluru and Kata Tjuta National parks. Until relatively recently waterbodies in this remote region were not well studied, even though most have deep cultural significance to local Aboriginal people. The region also contains some of the highest densities of feral camels in the nation, and was a focus area for the recently completed Australian Feral Camel Management Project. Within the project, the specific impacts of feral camels on waterholes were assessed throughout the Petermann ALT. We found the aquatic invertebrate biodiversity was significantly lower at camel-accessible sites, and fewer aquatic species considered “sensitive” to habitat degradation were found at sites when or after camels were present. In addition, the water quality at camel-accessible sites was significantly poorer (e.g., more turbid, more DO supersaturation, etc.) than at sites that camels could not access. The results of a multi-year camera trap study at the same waterholes suggest that camels can trigger a “competitive cascade” whereby native species are displaced by apex predators that have been displaced by camels. These results, in combination with emerging research and anecdotal evidence, suggest that large feral herbivores, such as camels and horses, are the main immediate threat to many waterbodies in central Australia. Management of large feral herbivores will be a key component in efforts to maintain and improve the health of waterbodies in central Australia, especially those not afforded protection within the national park system.