Restriction to the freshwater environment plays a dominant role in the population genetic structure of freshwater fauna. In taxa with adaptations for terrestriality, however, the restrictions on dispersal imposed by drainage divides may be overcome. We investigate the mitochondrial phylogeographic structure of the eastern long-necked turtle (Chelodina longicollis), a widespread Australian freshwater obligate with strong overland dispersa\l capacity and specific adaptations to terrestriality. We predict that such characteristics make this freshwater species a strong candidate to test how life-history traits can drive gene flow and interbasin connectivity, overriding the constraining effects imposed by hydrological boundaries. Contrary to expectations, and similar to low-vagility freshwater vertebrates, we found two ancient mitochondrial haplogroups with clear east-west geographic partitioning either side of the Great Dividing Range. Each haplogroup is characterised by complex genetic structure, demographically stable subpopulations, and signals of isolation by distance. This pattern is overlaid with signatures of recent gene flow, likely facilitated by late Pleistocene and ongoing anthropogenic landscape change. We demonstrate that the divergent effects of landscape history can overwhelm the homogenising effects of life-history traits that connect populations, even in a highly vagile species.