Major sections of today’s rivers are man made and do not provide the essential requirements for riverine fish. A nature-like fish by-pass system in Vienna-Freudenau was assessed for its function as a fish habitat. The study was conducted continuously over 3 years; 15 years after construction of the by-pass. The chosen nature-like construction of the by-pass system functions like natural tributaries. More than 17000 fish and 43 species, including several protected and endangered species, in all life stages, including eggs, larvae, juveniles and adults, were captured. Furthermore, the indicator species of the free-flowing Danube, nase (Chondrostoma nasus) and barbel (Barbus barbus), migrated into the fish by-pass and successfully spawned before returning. Therefore, our results suggest that by-pass systems can function as an important habitat for the conservation of native fish fauna. The heterogenic habitat configuration provides conditions for all ecological guilds and, consequently, increases biodiversity. Finally, approved management tools are discussed. We suggest that fish by-pass channels may be suitable at other sites in the Danube catchment.