Lake water level fluctuations (WLF) are an important factor driving the selection and seasonal dynamics of phytoplankton and potentially toxigenic cyanobacteria. Nevertheless, the relative importance of environmental drivers connected to WLF may be completely different, depending on the typology and use of waterbodies, latitude and climatic regimes. In this study, we investigated the impact of WLF in a large subtropical reservoir in south-eastern China (Hongfeng Reservoir, Guizhou Province). The study was based on monthly samplings carried out in 2014 in six stations. The strong increase in the water level observed in early summer caused a radical shift in the phytoplankton community. While in the pre-flooding period phytoplankton was composed of large diatoms, chrysophytes and Oscillatoriales (mostly Limnothrix sp.), the post-flooding period showed an increase in smaller and more competitive chlorophytes, smaller diatoms and cryptophytes better adapted to a fast colonisation of new and nutrient-rich environments. The environmental drivers that drove the change were dilution, flushing and interference with the seasonal water stratification processes. We concluded that, because WLF represents a complex variable integrating different physical effects in one explanatory descriptor, its value as a predictor of phytoplankton and cyanobacteria dynamics in lake ecosystems is difficult to generalise and needs to be investigated on a case-by-case basis. For this reason, considering the year-to-year hydrological variability that potentially characterise reservoirs, definite indications for management should be outlined considering more than 1-year study.