Central Australia (CA) has an arid environment characterised by low and unpredictable rainfall, high temperatures and high evaporation rates. Within this desert context reliable water features, sustained mainly by natural groundwater discharge, provide distinct and isolated habitats for both aquatic and terrestrial species, even where these features are only minimally inundated. CA water features are varied, and include springs, waterholes and seepages that provide refuge for relict, endemic, and widely dispersed species confined to discontiguous habitats. They have been well known to Aboriginal people for thousands of years, and are often sites of great cultural significance. In spite of their biological, cultural and economic importance, the physical and ecological characters of many waterbodies are not well known. CA has experienced some of the most rapid rates of warming observed on the Australian continent. Successfully managing the consequences of climate change in CA will depend, in part, on developing a better understanding of the factors that influence long-term biodiversity in these aquatic systems. Because isolated CA waterbodies are at the forefront of continental warming, they could provide insights into how climate change will potentially impact other arid zone aquatic ecosystems.