To effectively improve the water quality of the Bai River, this paper proposes the use of the ecological replenishment of the South–North Water Transfer as a measure for the integrated allocation of water resources, addressing the impact of complex topography, climate, and human disturbances on the river’s water environment. This measure can alleviate the problem of water shortage and significantly enhance the quality of the Bai River’s water environment. Using the MIKE21 coupled hydrodynamic and water-quality model, this paper analyzes the impact of ecological recharge on river hydrodynamics and simulates the evolution of various water-quality indicators, including dissolved oxygen (DO), permanganate index (CODMn), chemical oxygen demand (COD), ammonia nitrogen (NH3-N), and total phosphorus (TP) under different scenarios. The aim of this paper is to investigate the impact mechanism of ecological recharge on the river’s water environment. The results show that the most significant improvement in river water quality is achieved when the recharge flow is 2Q and the recharge duration is 1/2T (scenario 1), with the river improving from a grade IV water-quality standard to a grade III water-quality standard, and COD and TP indicators improving to a grade II water standard, with the largest improvement rate of 94.67% seen in DO, with the best improvement rate of 94.67% in DO indicators and the best reduction rate of 66.67% in TP indicators. Overall, ecological replenishment can significantly improve the Bai River’s water quality, with scenario 1 being the most effective approach. The results of this study may provide theoretical and technical support for the future management of river water environments.