Ecosystems often show sudden and drastic shifts in their states following relatively small environmental changes, yet the environmental restoration does not necessarily easily recover the original state. The resilience theory has played a pivotal role in ecosystem management by providing a theoretical basis for such abrupt and irreversible phase transitions (i.e., regime shifts). However, a major concern remains that the existing theory considers ecosystem responses along only a single disturbance axis (e.g., eutrophication), despite the fact that natural ecosystems are subject to multiple anthropogenic disturbances. In this study, I introduce ontogenetic niche shifts as a possible common mechanism of regime shifts. Based on this framework, I show how additional factors not accounted for the basic resilience theory (e.g., species extinction and invasion, habitat loss and fragmentation, and phenological shifts) may affect whether or where regime shifts occur along the environmental gradient. My results taken together illustrate the importance of interdisciplinary research integrating biodiversity conservation, landscape protection, and climate change adaptation for more effective management of lake ecosystems.