The flow regime is a determinant of the ecological function and natural dynamics of a river system with a prominent effect on freshwater fish. Here, we introduce a number of contributions to the Special Session, “Ecohydraulics of river flow alterations and impacts on freshwater fish,” that occurred at the XIX Conference of the Iberian Association of Limnology. The multidisciplinary contributions illustrate the impacts of river flow alteration on aquatic biota, describe mitigation measures and restoration actions to address river flow regulation, and present innovative tools for research in the ecohydraulics field. The research topics debated included environmental flows, river restoration, hydropeaking impacts on aquatic organisms, innovative methods and devices, and hydropeaking mitigation strategies. The importance of ecohydraulics as an emerging science was debated. The bridge between the disciplines of limnology and ecohydraulics was highlighted to understand flow alteration impacts and provide solutions to mitigate those impacts. This Special Session provided an opportunity to embrace ecohydraulic scientists in limnology research.