European freshwater fishes and mussels have experienced serious declines, both in terms of their spatial distributions and their population sizes. Captive breeding can be an important rescue tool to bridge critical life stages such as insufficient reproduction in the wild, and stocking of captive-bred animals can help to increase populations sizes above the viable minimum. This contribution addresses how such conservation-oriented captive breeding programmes can be most effective by creating synergies between science and practical application. Using the examples of the endangered freshwater pearl mussel (Margaritifera margaritifera), the Danube salmon (Hucho hucho), and the European nase (Chondrostoma nasus), the usefulness of genetic monitoring in such programmes will be highlighted. This includes the deduction of guidelines for the informed choice of source populations and parents based on genetic pre-screening, and the consideration of selection, genetic drift and adaptation to certain environmental conditions during the breeding and rearing process. The examples will also be used to illustrate possible pitfalls such as inbreeding and outbreeding effects as well as measures to avoid such effects. The three presented case studies show that conservation-oriented captive breeding needs to be managed differently than classical food-production oriented aquaculture systems, e.g. in terms of in terms of the spawners' origin, numbers, sex rations and exchange rates. Rearing conditions need to mimic natural habitat and avoid selection of features that are disadvantageous in the wild. The findings also suggest that, depending on the differences in life histories of the species, multiple production cycles and long-term programmes can reduce the risk of deleterious genetic effects. Many populations of freshwater fishes and mussels would go extinct in the nearby future without captive breeding and stocking actions, but any captive breeding action must be run in concert with habitat conservation and restoration to ensure long-term population sustainability.