Large-scale water diversion has, to a certain extent, altered the hydrological conditions in the water discharge area, disrupting the long-established hydrological consistency and, in turn, impacting the ecological environment. In this study, we utilized satellite imagery and underwater topographic data of the Three Gorges Reservoir Area (TGRA) to construct a coupled hydrodynamic-water quality-aquatic ecology model based on MIKE21. We simulated and analyzed the water environmental conditions at two crucial sections, Cuntan and Wanzhou, under different water diversion scenarios. The research findings indicate that under both short-term and long-term water diversion scenarios, the pollution levels at both sections have increased, with pollutant concentration varying between 0 to 0.0217 mg/L and 0 to 0.0642 mg/L throughout the year. Long-term water diversion has a more significant impact than short-term diversion, particularly with a longer duration of influence during the winter. The impact of water diversion on water quality classification is not very pronounced. It primarily reduces the number of days when Class I water quality is achieved. Under short-term and long-term water diversion scenarios, the proportion of days with Class I water quality at the Cuntan and Wanzhou sections decreased by 0.28% and 0.55%, and 0.56% and 0.83%, respectively. These research results can serve as a theoretical foundation for further developing ecological risk mitigation strategies and establishing an eco-friendly inter-basin scheduling model.