As an important water supply reservoir for Dongguan and Shenzhen, the water quality of the Bai Ni Keng channel, which feeds into the Yan Tian Reservoir, does not meet the standards throughout the year, making it difficult to meet the water quality requirements of the Yan Tian Reservoir as a drinking water source. This paper constructs a one-dimensional hydrodynamic and water quality model for the Bai Ni Keng channel, analyzing the improvement effect of the newly constructed engineering measures on water quality. It was found that when the Bai Ni Keng channel encounters a 3-year, 50-year, and 100-year design flood, the main pollutants entering the Dong Shen channel through the newly constructed box culvert do not meet the surface water class V during the early stages of discharge (about 6 h), including total phosphorus, COD, total nitrogen, and ammonia nitrogen. As the discharge volume increases, the concentration of each pollutant decreases, and at the flood peak, it can reach the surface water class III. Therefore, the implementation of the project will have a certain impact on the water quality. Based on real-time water quality conditions, appropriate positions can be selected for flood regulation to reduce the flood discharge impact on the downstream river channels.