A numerical simulation of groundwater dynamics in the Sugan Lake Basin was conducted by using MODFLOW, and 50-year predictions were made for four different water diversion schemes. The results from MODFLOW simulations fit well with the measured data, indicating that the established model can be used for predicting the groundwater dynamics in the Sugan Lake Basin. The MODFLOW simulation results under different water diversion schemes reveal that over a period of 50 years, as the amount of diverted water increases, the shrinkage rate of the large Sugan Lake's area also increases, and the groundwater level in the Sugan Lake Basin shows a general declining trend. The impact of inter-basin water transfer exhibits certain time lags and spatial heterogeneity. Considering both the water diversion requirements and the effects of the water diversion project on the ecological environment of the Sugan Lake Basin, it is suggested that a water diversion scheme of 1.0 × 10⁸ m³/a is more appropriate. The research results provide important scientific theoretical support for assessing the impacts of inter-basin water transfer projects on the ecological environment of the Sugan Lake Basin and for determining suitable water diversion schemes.