Lake currents have an important impact on distribution of pollutant concentrations in large shallow lakes. Taking Taihu Lake as an example, in view of the characteristics of wind-driven water flow in the lake, this paper puts forward a water environmental capacity calculation method that uses wind direction and wind speed combined frequency to provide joint correction and pollution zone control for the designed hydrological conditions. In the study, the total length of the pollution belt was controlled to be 10% of the length of the study area, and a mathematical model of two-dimensional unsteady water quantity and quality in Taihu Lake was established. By analyzing the hydrological water quality characteristics and measured data of Taihu Lake in recent years, the flow field and concentration field were simulated and verified, the mathematical model and the plausibility of the parameters were calibrated. The water environmental capacity of Taihu Lake basin was calculated by this method. The calculated results showed that the water environmental capacity of chemical oxygen demand (COD), total phosphorus (TP), and total nitrogen (TN) in Taihu Lake were 113,331 t·a−1, 479 t·a−1 and 6,521 t·a−1. By providing a technical basis for total pollutant control and management in Taihu Lake basin, this study is conducive to the planning and management of water environment.