Groundwater and surface water-fed systems act as biodiversity hotspots and aquatic refugia in central Australia. Groundwater is the essential resource supporting perennial and long-lasting waterbodies, whilst surface-fed systems tend to be temporary or ephemeral. The critical role perennial waterbodies play in supporting plant and animal communities in arid regions, and their persistence under predicted future declines in rainfall associated with global warming, highlights the need to determine which systems are groundwater-dominated. We used isotope hydrology, with water sampling undertaken by citizen scientists, to determine the relative dominance of groundwaters and surface waters in waterbodies in arid central Australia. Volunteer citizen scientists were given a sampling pack containing instructions, vials and labels. Over 240 water samples were submitted to the Outback Water Project, from 62 unique sites spanning an area across central Australia of >250,000 square kilometres. Approximately 75% (182) of the samples were collected by citizen scientists and 25% (60) by research scientists. It is unlikely that so many samples could have been collected across such a large area without the help of citizen scientists. Samples were analysed for electrical conductivity (EC) and isotopic composition (δ18O & δ2H) using IRIS (isotope ratio infrared spectrometry). From this dataset we identified 20 perennial groundwater-fed waterbodies (δ18O < -3 ‰) that are likely to contain water throughout the most severe of droughts. These waterbodies will be critically important for the persistence of water-dependent species and should be prioritised for management and restoration. All sites identified as future refugia were located within protected areas including Tjoritja/West MacDonnell Ranges National Park,Watarrka National Park, Finke Gorge National Park and Indigenous Protected Areas (IPAs). However, despite their protected status, some sites are subject to the impacts of feral species, including camels (Camelus dromedarius), horses (Equus caballus), cats (Felis catus), foxes (Vulpes vulpes) and invasive plants (buffel grass, Cenchrus ciliaris). Our findings indicate where control programs and restoration actions could be prioritised as part of biodiversity conservation strategies and climate change adaptation programs. Our approach, combining the sampling power of citizen science and relatively inexpensive isotope hydrology, could help identify future aquatic refugia in other remote and arid regions where water scarcity is likely to increase under global climate change.