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Shallow lakes, one of the most widespread water bodies in the world, are easily shifted to a new trophic state due to external interferences. Shifting hydrologic conditions and climate change can cause cyanobacterial harmful algal blooms (CyanoHABs) in shallow lakes, which pose serious threats to ecological integrity and human health. This study analyzed the effects of hydrologic and meteorological variables on cyanobacterial blooms in Yangtze-connected lakes (Lake Dongting and Poyang) and isolated lakes (Lake Chao and Tai). The results show that (i) chlorophyll-a (Chl-a) concentration tends to decrease exponentially with increasing relative lake level fluctuations (RLLF) and precipitation, but to increase linearly with increasing wind speed and air temperature; (ii) Chl-a concentrations in lakes were significantly higher when RLLF 2.6 m s−1, or air temperature > 17.8 °C; (iii) the Chl-a concentration of Yangtze-isolated lakes was more significantly affected by water level amplitude, precipitation, wind speed and air temperature than the Yangtze-connected lakes; (iv) the RLLF and the ratio of wind speed to mean water depth could be innovative coupling factors to examine variation characteristics of Chl-a in shallow lakes with greater correlation than single factors.