Freshwater ecosystems in arid regions range from highly fragmented to highly connected, and connectivity has been assumed to be a major factor in the persistence of aquatic biota in arid environments. This review sought to synthesize existing research on genetic estimation of population connectivity in desert freshwaters, identify knowledge gaps, and set priorities for future studies of connectivity in these environments. From an extensive literature search, we synthesized the approaches applied, systems studied, and conclusions about connectivity reached in population genetic research concerning desert freshwater connectivity globally. We restrict our scope to obligate aquatic fauna that disperse largely via freshwaters and exclude those with active aerial dispersal abilities. We examined 92 papers, comprising 133 studies, published from 1987 to 2014. Most described studies of fishes and invertebrates in the deserts of Australia and North America. Connectivity declined with increasing scale, but did not differ significantly among arid regions or taxonomic classes. There were significant differences in connectivity patterns between species with different dispersal abilities, and between spring and riverine habitats at local scales. Population connectivity in desert freshwaters is typically most influenced by the ecology of the species concerned and hydrological connectivity. Most studies did not assess predefined models of connectivity, but described gene flow and/or genetic structure. Climate change and anthropogenic impacts worldwide are likely to increase the incidence and impact of habitat fragmentation in already threatened desert freshwaters. To reduce this risk, biodiversity conservation and environmental management must address connectivity, but often the required information does not exist. Researchers can provide this by explicitly considering the effects of hydrology and species’ ecology on connectivity, and incorporating these into connectivity models, which are vital for understanding connectivity in desert freshwaters.