The ecological, evolutionary and genetic attributes of species develop within the environmental contexts in which they evolve, and are geared to them. Understanding how species occupy and move around their habitats in space and time is of fundamental interest in ecology. It is also a key platform by which to understand how the projected population persistence of species might change under human impacts, which typically alter population connectivity. In the context of freshwater systems, hydrological connectivity in space and time is a key driver of species ecology and evolution. Human impacts tend to change – increase, decrease and alter the patterns of – hydrological connectivity, as well as the nature and extent of freshwater habitat. Estimating dispersal of organisms can be extremely challenging; genetic techniques, and recently genomic ones, can offer very substantial assistance here. Furthermore, these approaches are the only way to understand to what extent evolutionary connectivity (gene flow) accrues from dispersal. Simultaneously, genomic approaches allow us for the first time to make comprehensive assessment of evolutionary history, future evolutionary potential, and to understand the distributions of ecologically important genetic variation that impact population fitness and persistence. In this presentation, I outline some of the key aspects of ecology and evolution that are readily assessed by genomic approaches, with examples taken from current research programs on invertebrate and fish species in the paradoxical, beautiful but threatened Australian arid zone freshwaters, and endangered iconic freshwater fish in eastern Australia.