The groundwater springs fed by the Great Artesian Basin in central Australia are home to a suite of endemic plants and animals. The species within these springs have evolutionary roots stretching back to before central Australia was a desert; when animals such as flamingos and crocodiles existed in permanent freshwater rivers, swamps and lakes. Unfortunately, inappropriate groundwater use has dried up around 2/3 of flowing springs, whilst those continuing to flow have suffered due to severe mechanical modification, stock and feral animal access and invasive species. Accordingly, this unique ecosystem has been afforded EPBC listing as an endangered ecosystem. Despite this listing, pressure for water continues, and only a small handful of springs are protected in national parks. With the majority of species within the springs being short-range endemics, some are at risk of complete extinction from the degradation of a single spring. Using phylogenetic analyses with community and species distribution data in combination with physical parameters, we can prioritise springs critical to the both the persistence of short-range endemics and the preservation of a species-rich desert spring fauna. This information will be used for the ongoing management of springs, and to prevent future water extraction from having detrimental impacts on spring animals.