Wind waves in shallow lakes are of great significance to lake ecosystems. Based on the synchronous high-frequency observation data in Lake Chaohu, the fast-changing characteristics of wind waves and their impacts on the water environment were analyzed in detail. The significant wave height and the average period of wind waves had a good synchronous response with the wind speed. In the phase of wind speed fast decline, the wave period has better stability than the wave height. The pH, water temperature, and dissolved oxygen will respond quickly to the changes of wind waves. As the intensity of wind waves increasing, the disturbance of water turbidity and total phosphorus concentration gradually appeared. The lag time of water turbidity changes caused by strong wind waves disturbance could reach 3 d. Strong wind waves disturbance would change the inherent distribution characteristics of physical and chemical parameters and the regular distribution of algae under fast-changing wind waves, indicating that the intensity of wind waves is the primary factor causing this difference.