Using historical sources from the turn of the 19th to the 20th century, we investigated the long-term evolution of the fish community in a mountainous river network and the influence of different human uses and management measures. Within the alpine Salzach catchment, historical presence was reconstructed for 26 fish species, abundance classes for 19 species. Due to channelization, flood protection and dam erections, the spatial distribution of fish species was reduced during the 20th century. Many rheophilic and eurytopic fish species historically inhabited river reaches along a wide longitudinal profile and were present in more upstream river reaches than nowadays. The decrease of species diversity in the headwater sections is a consequence of lost lateral connectivity. Strongest effects are reported for sensitive species requiring different habitat types during their life cycles (especially pike, nase, Danube salmon). One of the most important shifts from the historical fish community to the present one reflects the deliberate introduction of fish species for fisheries. Rainbow trout and brook trout, absent from the historical fish assemblage, today represent up to 29 % of the total number of fish occurrences. In contrast, log driving, one of the most common historical pressures in European mountainous rivers, did not show significant negative effects on the past fish ecological situation. This result strongly differs from the impacts of log driving and deforestation demonstrated for recent times, and could be related to the change in log driving practices during the 20th century and to the high societal value of fish before the industrialization period along with other historical pressures affecting fish in rivers without log driving. In general, our results can be valid for a large number of European mountainous rivers. They highlight the usefulness of such detailed historical studies for our understanding of the long-term evolution of fish communities and their present functioning, and point the way for future river management strategies to restore fish biodiversity.