Global lake systems have undergone rapid degradation over the past century. Scientists and managers are struggling to manage the highly degraded lake systems to cope with escalating anthropogenic pressures. Improved knowledge of how lakes and social systems co-evolved up to the present is vital for understanding, modeling, and anticipating the current and future ecological status of lakes. Here, by integrating paleoenvironmental, instrumental and historical documentary resources at multi-decadal scales, we demonstrate how a typical shallow lake system evolved over the last century in the Yangtze River Basin, an urbanized region containing thousands of shallow lakes. We find abrupt ecological shift happened in the lake ecosystem around the 1970s, with the significant reorganization of macrophyte, diatom and cladocera communities. The lake social-ecological system went through three stages as the local society transformed from a traditional agricultural before 1950s to an urbanized and industrialized society during the recent thirty years. The timing and interaction between social, economic and ecological feedbacks govern the transient and long-term dynamics of the freshwater ecosystem. Our results highlight the importance of accounting for the long-term dynamics and feedbacks between ecological, social and economic changes when defining safe operating spaces for sustainable freshwater ecosystem management.