While dispersal and connectivity are crucial processes for individuals and species, a range of systems remain understudied and our understanding of the behavioural underpinnings is limited. Moreover, natural habitat patches are rarely homogenous over space and time, meaning that understanding movement responses can be complex. The desert goby Chlamydogobius eremius is a remarkable fish endemic to arid South Australia, a naturally dynamic environment in which water is scarce and fragmented, and large expanses of dry land comprise the major barriers to aquatic dispersal. Additionally, habitat variation can be partitioned into two characteristic ‘types’: permanent, groundwater-fed springs, and highly variable, highly ephemeral rivers. Consequently, spring and river fish are likely to experience different costs and benefits of dispersal, and potentially, divergent selection regimes and opportunities for movement. We examined the effects of habitat variation on dispersal using both molecular and behavioural approaches. Using a comparison of populations from springs and rivers, I will present i) the results of a mitochondrial DNA-based phylogeography for the species, and ii) experimental data on exploratory and dispersal (emigration) propensities. While we found that some springs contained higher levels of genetic diversity, our behavioural measures detected limited evidence for adaptive shifts in dispersal and exploration. Thus, despite strong potential for divergent selective environments, it appears that dispersal behaviour in the desert goby conforms to a traditional prediction of high phenotypic plasticity, an important mechanism in potentially mediating impacts of future environmental change.