Natural and human disturbances have caused widespread regime shifts in shallow lakes of the lower Yangtze basin (LYB, China) resulting in a severe decline of ecosystem services. Improved understanding of the relationship between environmental forcing and ecosystem response, and the mechanisms behind regime shifts has significant implications for management. However, the patterns of these regime shifts and the underlying internal mechanisms, are less known. In this study, two typical lakes (Chaohu and Zhangdu) from the LYB were selected to determine the trajectories of ecological regime shifts, both of which transitioned from vegetation- to plankton-dominated states several decades ago. Ecological trajectories since the 1900s in both lakes were reconstructed using palaeolimnological proxies, mainly diatom assemblages. Although results show that regime shifts occurred in both lakes in the 1970s and the 1950s respectively, their inherent mechanisms were different. In Lake Zhangdu, altered hydrological conditions pushed the ecosystem across an ecological threshold, providing an example of a driver-mediated regime shift. In Lake Chaohu, ongoing nutrient loading influenced ecosystem processes and drove the lake to an alternative stable state, potentially presenting an example of a critical transition after a loss of resilience. This research indicates that palaeolimnological perspectives can provide insights into regime-shift changes, as well as important information regarding which restoration methods should be tailored to individual lakes.