Aridification has driven significant environmental change in central Australia over millennia. Most of the Australian continent did not undergo the extensive Pleistocene glaciation experienced in the Northern Hemisphere. Instead, ongoing aridification resulted in perennial freshwater systems in the arid interior contractingto isolated groundwater-fed springs and a network of intermittently flowing rivers. The latter exist as isolated waterholes for most of each year. We recently completed the first study of the microbiomes of arid zone outcrop springs and riverine waterholes in central Australia. Our results suggest that local, rather than landscape processes, are an important driver of the composition of the microbiomes at these sites. We found that the composition of biofilm microbial communities varied greatly within a site, whilst the water column microbial communities were more homogenous and displayed considerable site fidelity. A much larger spatial study (over the entire arid biome) is now planned to better understand the patterns and processes driving arid zone aquatic microbial communities.