The legacy of historic anthropogenic disturbance can significantly affect the structure and function of contemporary freshwater ecosystems. Environmental research and management that neglect anthropogenic legacy are likely to lead to a biased interpretation of present and future ecosystem dynamics. Yet, anthropogenic legacy remains poorly considered, mainly because of the challenges associated with its identification. Synthesizing past progress in legacy research, we present a conceptual framework for the systematic identification of anthropogenic legacy. We focus on the dynamic processes occurring during legacy formation (e.g., disturbance regime, ecosystem trajectories). Based on the review of relevant case studies, we discuss the historical and contemporary sources of information (e.g., communication, cartographic, paleoenvironmental sources) that can be employed for legacy identification. Finally, we provide practical examples of anthropogenic legacy identification in real-world freshwater ecosystems. Produced in multidisciplinary collaboration, this review presents a comprehensive approach to anthropogenic legacy to foster its informed and systematic consideration in freshwater research and management.