To explore the impact mechanism of water level fluctuation on water quality in shallow lakes, taking the Huayang Lakes as the research object, the water level data, and the water quality data of nitrogen and phosphorus nutrients, chlorophyll-a, turbidity and so on are collected, Pearson correlation analysis and the principal component analysis (PCA) are employed to analyze the correlation between water level and water quality indicators, and the effects of water level fluctuation on endogenous release and phytoplankton are discussed. The results indicate that the water quality of Huayang Lakes exhibits obvious features of seasonal and spatial variations. Overall, water level is negatively correlated with total nitrogen and total phosphorus, and positively correlated with chlorophyll-a. The turbidity is significantly positively correlated with total phosphorus, and significantly negatively correlated with chlorophyll-a. During the low water level：sediment resuspension is enhanced，leading to an increase in nutrients； the turbidity is increased, leading to a decrease in light intensity, which in turn causes a decrease in chlorophyll-a. The research results can provide reference for better understanding the relationship between water level and water quality in shallow lakes, and provide scientific basis for lake management and protection.