We review the status of the freshwater fish fauna of Patagonia, an assemblage with 26 native species, comprising fishes of Gondwanan origin, marine dispersants, and oceanic elements of local origin. Several processes, old and new, have shaped the landscape of Patagonia and its fauna: a Gondwanan heritage, the Andes uplifting, Pleistocene ice, volcanic activity, introduction of exotic fishes, mostly Salmonids, and climate change. While there is a significant tradition of taxonomic work on native fish species, research on life history, trophic relationships, and community structure has started to emerge only in the last 15 years. Most studies were conducted in oligotrophic lakes of the Andes; while fauna of streams remains poorly observed. While documentation of impacts by salmonids is scarce, there is some compelling evidence indicating that freshwater communities have been significantly shaped by exotic fish. Impacts by exotic species appear to be dependent on temperature on the east side of the Andes, and land use and watershed perturbation on the west side.In general, freshwater habitat conditions and how they affect fishes are poorly studied. In lakes, habitat complexity and its specialized use by native fishes may have ameliorated the impact by introduced salmonids. Although impacts on rivers abound, led by dam construction, the relationship between stream habitat integrity and native species health is still poorly understood. The future of freshwater resources will largely depend on how able we are to inform managers, the general public and colleagues about their value and the costs of not taking action. But current research capacity is insufficient to deal with most demands because of limitations in people, resources and baseline information. To support our claims, we need to promote regional assessments of freshwater resources and of major threats to their integrity, the building blocks of a regional agenda for their sustainable use.