Abstract: The terrain of mountain river boundaries is complex, the hydrodynamic conditions change drastically, and hydrological and water quality data are lacking, leading to significant uncertainty in the water environment system. Conducting numerical simulation research has important scientific and practical significance. In this study, we established a MIKE 21 hydrodynamic and water quality model based on the Navier−Stokes equations to perform numerical simulations of the water environment in the Gulin River, a typical mountain river in the southern part of Sichuan Province. The results show that the established model performs well, with an average coefficient of determination (R²) of 0.93 for the hydrodynamic model and an average mean relative error (MRE) of 14.25%. For the water quality model, the average R² is 0.86 and the average MRE is 19.83%. Hydrodynamic scenario simulations show that doubling the rainfall increases the average flow velocity at the control section by 7.94%, while doubling the wind speed increases the average flow velocity at the control section by 5.26%. Under different water supplementation scenarios, when the supplementation locations are 5 km upstream of the Deyao Town, Gulin Town, and Taiping Town wastewater treatment plants, and the supplementation amount is 50% of the treatment plant capacity (0.29 m³/s, 0.58 m³/s, 0.46 m³/s), the average concentrations of COD, NH₃−N, and TP at the control section decrease the most, by 24.55%, 25.25%, and 26.79%, respectively. The research results can provide references for the study of mountain river water environments and are of significant importance for the management of water environment systems in mountain rivers.