The Dragon lake diversion channel (DLDC) is the only river that recharges Dragon Lake, an artificial lake in China. This paper examines the main factors influencing water quality by investigating point source and non-point source pollutants along the main route. Based on the complicated system of rivers and desilting basins, a three-dimensional water quality model using environmental fluid dynamics code (EFDC) was developed. The model of DLDC was calibrated and verified using observed data. The error ranges of river water level, total phosphorus, total nitrogen and chemical oxygen demand were within 5%, 10%, 16% and 20%, respectively, all of which meet the precision requirement. The model was employed to predict the concentrations of pollutants in the main stream under current pollution loads within a year and a flood lasting for 24 hours. The results revealed that the main pollution sources that influence the water quality of waterways were the point sources followed by the non-point pollution sources. Water quality improved when large water quantities were delivered and this trend can be described as dilution. The water quality of the Dongfeng main channel meets the requirement; however, the water quality of the Dongfeng River is somewhat poor, and the water quality of the Wei River is seriously contaminated. To address these problems, we suggest that the Dongfeng River and Wei River adopt a culvert under its riverbeds.