Aim: Those locations and features providing refugia for species during unfavourable climatic phases may be important to identify and conserve to help protect biodiversity in the near future. During the Pleistocene, climates oscillated between glacial and interglacial periods. In the Northern Hemisphere, the impact from glacial ice sheets caused species to disperse to warmer southern refugia, but less is known about changes to species' distributions during these periods in the Southern Hemisphere. Location: In Australia, the climate alternated between highly arid and wetter periods during the Pleistocene. It has been proposed that arid refugia may be associated with the inland ranges (areas of higher relief), the mesic east, or areas that maintained favourable species-specific ecological conditions. We tested these hypotheses with a phylogeographical analysis of a widely distributed tree-dwelling gecko, Gehyra variegata (2n = 40a chromosomal race) throughout the central and eastern regions of arid Australia. Methods: We generated a mtDNA sequence and microsatellite dataset by sampling 740 G. variegata40a throughout its known distribution. We also use species distribution modelling to predict the species' likely past, present and future distribution. Results: The majority of G. variegata40a lineages diverged during the Pleistocene, and those located in regions of arid Australia where mean annual water run-off is highest, displayed higher levels of genetic diversity in comparison locations with lower run-off. We also show that genetic diversity increased with proximity to water sources. Main conclusions: It is likely that G. variegata40a contracted to refugia associated with stable water sources during Pleistocene arid phases. However, modelling suggests that unfavourable climate conditions will be present in this region by 2070. Therefore, Pleistocene refugia for G. variegata40a are unlikely to be refugia in the future. More generally, our results suggest that water run-off could be a useful predictor to identify favourable conditions for some arid species.