In many large shallow lakes across the globe, the surface wind field drives the hydrodynamic process directly through the momentum and energy exchange at the air–water interface. Numerous field measurements, experiments and modeling show that wind-driven hydrodynamic disturbances have profound impacts on the structure and function of lake ecosystems. In this article, we review the response of the shallow lake to the wind-driven wave and flow field, which may accelerate the sediment resuspension and nutrient cycling and, in turn, affect the concentrations of nutrients and dissolved oxygen. Furthermore, the life activities of bacterioplankton, plankton and fish in the aquatic ecosystem are closely related to these water-quality factors. Although we have a developed understanding of the physical processes and biogeochemical cycles of lakes by process-based modeling, the most basic wind-driven hydrodynamic process in some lake models is imprecise. Comprehensive results of physical parameterization, including the wind stress and wind drag coefficient, with their mathematical expressions for depicting the wind-driven force in the hydrodynamic model of lakes are synthesized. Some of these expressions are empirically determined without considering the dynamic environment, and expressions based on physical mechanisms have been widely recognized. Additionally, the adaptation standard of wind-driven force parameterizations to inland lake models under light winds is provided. This article highlights the importance of heterogeneous wind field variability and suggests future studies on the wind fields in extreme climates, which could also cause damage to deep lake ecosystems and the biodiversity effects of wind wave turbulence.