Fish passes facilitate fish movement in fragmented river systems, yet they can also provide important habitat functions. This study investigated the fish community composition of different constructed habitat types (fluvial habitats, floodplain ponds) within fish passes in relation to habitat characteristics in order to deduce recommendations for fish-friendly designs of such structures. Fish community structures within passes differed significantly from those in the main river, comprising a high number of rheophilic species in fluvial habitats (Thymallus thymallus, Hucho hucho, Salmo trutta, Cottus gobio, Chondrostoma nasus, and Barbus barbus), and of stagnophilic species in floodplain ponds (Rhodeus amarus, Scardinius erythrophthalmus, Misgurnus bipartitus, and Tinca tinca). During summer, floodplain ponds also provided important juvenile habitats for the target species C. nasus and B. barbus. Differences between the two habitat types in fish abundance were mostly explained by differences in macrophyte coverage, gravel, boulders, temperature, and current speed. The findings of this study stress the important habitat functions of fish passes. They also suggest that integration of diverse habitat structures, especially of currently hardly considered constructed floodplain ponds into fish passes, can greatly enhance their fish communities and contribute to the restoration of several declining target species of conservation.