Australia’s largest and most important waterway- the Murray-Darling Basin (MDB) - is under threat owing to predicted increases in temperature extremes and reduction in rainfall - runoff in the coming decades. Management strategies are required that incorporate an understanding of dispersal patterns of the MDB fauna and flora. Patterns of dispersal have typically been studied through direct organismal studies but genetic approaches, in which the movement of genes in the landscape is used as a correlate of species dispersal, can provide a more comprehensive view by investigating at a much larger temporal and spatial scale. Genetic connectivity (dispersal) is influenced by the biology of the species, and by flow regime and the dendritic pattern of the network in riverine landscapes. An understanding of the relative influence of each on connectivity is required to deliver informed management strategies. Decisions regarding whether management for conservation is necessary also require an understanding of a species susceptibility to a changing environment. Species already exhibiting deleterious trajectories under current flow regimes in the basin may require more drastic measures than those that have remained unaffected.