The temporal dynamic of riverine ecosystems and their fish communities and populations has been addressed in ecological theory and management for several decades. A growing number of case studies on the historic development especially of European and North American rivers have been published. Nonetheless, a theoretical debate about the contributions and limits of historical approaches and interdisciplinary co-operation is lacking. This article presents a brief overview of the role of history in river and fish ecology and suggests historical ecology as a scientific field that can offer a framework for future research. Based on case studies compiled in this special issue on the “Historical ecology of riverine fish in Europe”, we draw conclusions on long-term changes of fish communities, on fisheries, aquatic ecosystem management and past habitat alterations and the potential of archaeological remains and written sources to study them. We discuss how modelling of historical fish data can help elucidate the effects of climate change and human influences on rivers and fish. Finally, we account for the necessity to consider appropriate spatial and temporal scales. In conclusion we call for future comparative studies on continental and global scales and methodological development, which can benefit especially from recent advances in marine historical ecology. We suggest that future interdisciplinary studies of ecologists, hydrologists, historians and archaeologists can reveal the history of riverine ecosystems as socio-ecological systems, addressing both their natural dynamics and human dimension. Such an endeavor can also support developing management plans for habitat restoration and conservation against the background of global change.