The dispersal of larvae and juveniles across a species’ range is a crucial component to maintaining population connectivity in many marine and freshwater fish species. When effectively maintained, this connectivity helps promote the genetic health of all connected populations, buffering them from both present and future abiotic and biotic stresses. The common galaxias Galaxias maculatus is a short-lived amphidromous fish species with an extensive larval marine phase. The spatial extent of larval dispersal is unknown for Victorian populations of common galaxias however, in other countries (e.g. New Zealand) populations have been shown to exhibit high dispersal rates during larval phase. We sampled returning juveniles from multiple rivers across the common galaxias’ range in Victoria. Our study uses highly resolving genomic techniques to characterise genetic diversity, population genetic structure and the spatial scale of juvenile dispersal among Victorian rivers. We investigate whether abundance estimates of juveniles returning to each river after their marine phase are correlated with levels of genetic diversity seen in each juvenile cohort. We provide new insights into relationships between abundance data and the genetic health of populations and the potential role of larval dispersal in maintaining genetic diversity in amphidromous fish species.