Central Australia supports a restricted but important range of freshwater systems, including small, permanent spring-fed streams and larger riverine pools ranging from permanent to ephemeral. These sites support a significant percentage of the aquatic and terrestrial biodiversity within the region. Comparison of records from the first exploratory scientific expedition to the area in 1894, and surveys conducted in 1986, 1994 and 2008, revealed the persistence of the aquatic invertebrate fauna, despite the recent impacts of European settlement. The presence of aquatic insects with Gondwanan origins suggests affinities with assemblages present in a much wetter era (∼18000 years ago). Persistence can be attributed to multiple environmental and social factors, including the role of local aquifers in sustaining permanent systems, the remote and inaccessible nature of the sites, and the protection and management afforded by reservation within national parks. Characterisation of the drivers and stressors that influence these ecosystems suggests that climate change could potentially result in a loss of endemic and relictual species. Hence, the relictual waterbodies of central Australia can be viewed as potential 'sentinel' sites for assessing the impacts of changing conditions.