Taking East Taihu Lake, an important shallow water bay of Taihu Lake, as an example, the influencing mechanism of wind waves on water quality in the shallow lake was discussed. The wind speed was translated into wave height using the classic wind-wave empirical formula to directly reflect the strength of wind wave, and the correlation relationships between the wind wave, polluted sediment rolling up, and water quality indices were analyzed. Results show that the water turbidity increases with the wind speed and wave height and is higher under the north wind. The concentration of DO decreases with the wind speed and wave height and is higher in winter and lower in summer. The concentration of COD increases with the wind speed and wave height and is higher in winter and lower in summer. The concentration of TN has no obvious correlation with the wind speed and is higher in summer and lower in winter. The water turbidity has good correlation with the concentration of COD. Study on the influencing mechanism of wind waves on water quality in the shallow lake can provide technical support for establishing lake water quality improvement measures.