AbstractThe global environment has experienced rapid changes over the past three decades, including global warming, global dimming and brightening, and abnormal climate fluctuations. However, direct evidence of global change in the regional physical environment of a lake is rare especially in China because long‐term observations are lacking. Here we demonstrate the profound changes in the physical environment of Lake Taihu using 25 years of long‐term meteorological, hydrological, and limnological observations and elucidate the potential implications for algal bloom outbreaks and aquatic macrophyte loss. We document significant increasing rates of 0.36 and 0.37°C/decade for the yearly mean air and water temperatures, respectively. In addition, significant increases are observed for the yearly total sunshine duration and yearly mean water level with the rates of 165.0 hr/decade and 0.15 m/decade. In contrast, significant decreases are documented for the yearly mean wind speed and Secchi disk depth with the rates of 0.27 m/(s · decade) and 0.21 m/decade for the macrophyte‐dominated regions, respectively. Therefore, the significant increasing ratio of temperature to wind promoted algal bloom formation and outbreaks, while the decreasing ratio of Secchi disk depth to water level resulted in the loss of aquatic macrophytes, which accelerated the shift from a clear macrophyte‐dominated state to a turbid phytoplankton‐dominated state in Lake Taihu. Forecasts of increased climatic variability in the future pose serious ramifications for both the ecosystem diversity and service functions of large shallow lakes. Our findings highlight the importance of long‐term physical environment monitoring data for understanding ecosystem response to global climate change.