As the world's population continues to grow, human water needs are growing accordingly, thus reducing the water available for sustaining our freshwater biodiversity. This is likely to be further exacerbated in areas where rainfall will decrease as a result of global climate change. Molecular ecologists have contributed substantially in recent years to our understanding of first, the levels and patterns of current biodiversity and second, to understanding patterns of connectivity among populations of aquatic species and their significance for their conservation and management. Both are critical for prioritisation of areas for protection and for designing rehabilitation programmes. In this paper, I attempt to synthesise our understandings to date. I argue that a multi-disciplinary approach that incorporates new technological approaches in acquisition of molecular data is the best way forward for our aquatic biodiversity. Molecular ecologists can contribute by collaborating with other ecologists, especially in the fields of species distribution modelling and conservation planning. This approach will help to prioritise conservation actions for the best possible outcomes.