Aquatic ecosystems in Central Australia are subject to boom-bust cycles, with the fauna, including insects, enduring long droughts and extreme flood events. During the drought phase, watercourses are reduced to a few disconnected pools, few of which are permanent. As a result, the habitats available to aquatic insects in Central Australia are highly fragmented both spatially and temporally. In this environment of highly variable connectivity, the ability to disperse successfully is likely to be a key factor for persistence. In multi-institutional collaborative research, focusing on seven insect species encompassing strong and weak dispersers, we will uncover patterns underlying dispersal traits, population genetics and landscape connectivity. By analysing up to 1400 anonymous nuclear markers per individual, we will identify fine-scale patterns of gene flow among spatially disconnected populations and infer the relationships among dispersal traits, environmental factors and functional connectivity of species in geographic space. Results from a preliminary study using single mitochondrial and nuclear DNA sequence markers indicate significant variation among populations of weakly dispersing species, while strong dispersers display minimal spatial genetic subdivision. However, the large volume of anonymous loci used in the current study will provide much more precise estimates of dispersal, gene flow and timing of these events among populations. The findings of this study illustrate the importance of permanent water and flooding events to the desert ecosystem, informing future management decisions in a region where water is a valuable commodity.