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Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South‐eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of river coalescence during low sea levels. Our specific hypothesis is that the degree of phylogeographic divergence between coastal river basins should correspond to the continental shelf width of each region. This predicts that genetic divergences between river basins should be lowest in regions with a wider continental shelf and that regions with similar continental shelf width should have similar genetic divergences. Pygmy …