As the consequences of global climate anomalies and the rapid development of hydraulic engineering, the hydrological condition of lake ecosystem has been greatly altered. By affecting the physico-chemical properties of water and sediment, the hydrodynamic variation can affect the survival, growth and distribution of submerged macrophytes. After long-term adaptive evolution, the submerged macrophytes have evolved a series of strategies to overcome the negative effects of hydrodynamic variation to a certain extent. However, at present, the degree of hydrological variation has far exceeded the adaptive capacity of the submerged macrophytes, and the catastrophic loss of submerged macrophytes has become a common phenomenon all over the world. Understanding the adaptive process of submerged macrophytes to hydrodynamic variation is the scientific basis for us to reveal the degradation mechanisms of submerged macrophytes and to design guidelines for their protection and restoration in the future. In this study, the cause of hydrodynamic variation in freshwater lakes, its consequences on submerged macrophytes, and the underlying mechanisms for submerged macrophytes to acclimate to the stress were summarized, including reproductive, morphological, and physiological strategies. Further studies on the anatomy and species-specific responses should be strengthened.