Alpine rivers are among the most heavily modified ecosystems in Europe. Following massive interventions in the 18th and 19th centuries, many plant species specialized in these challenging environments declined and are now endangered or even locally extinct. Today, attempts are being made to reintroduce these species as part of restoration measures, but only a few are successful. The selection of potential sites for reintroduction is commonly intuitive and based on practical considerations, while a prior scientific assessment of habitat availability and habitat connectivity is lacking. To increase the success of future reintroductions, we employ a habitat suitability model and subsequent habitat connectivity analysis to identify promising regions and patches for reintroduction within a riverscape. We demonstrate this approach using the Alpine river specialists Chondrilla chondrilloides and Myricaria germanica in three differently degraded and one restored section of the large Alpine river Isar. All river sections provide habitats for both species, but with increasing degradation, habitats become fewer and less connected. For the species with a narrower habitat niche and lower dispersal ability, suitable and connected patches that support a self-sustained metapopulation are only found in the near-natural sections. Despite an improvement in the habitat situation, the patch size in the restored section is too small, and the patches are too scattered to support a successful reintroduction of the species. We show that this evidence-based approach outperforms an intuitive selection of out-planting sites. The results further underline the importance of using scientific habitat analysis to increase the success of reintroduction measures.