A two-dimensional environmental fluid dynamics code(EFDC)model was established for the Shuikoubaxia-Jingangtui sections in the lower reaches of the Minjiang River. The parameters of the model were calibrated using synchronously monitored hydrological and water quality data. The model was used to predict the variation of the DO concentration in the lower reaches of the Minjiang River under different conditions. The results show that, to increase the split ratio of the North Channel, to decrease the domestic sewage and livestock wastewater from Minhou County, and to enable the water quality of the Guangming River and the Baima River to reach the grade Ⅴ level could result in the increase of DO in the North Channel. In contrast, DO decreased when the discharge from the Shuikou Reservoir was reduced. In order to ensure that DO in the lower reaches of the main stream of the Minjiang River reaches the standard continuously, the following measures should be taken: increasing the split ratio of the North Channel and the discharge from the Shuikou Reservoir in the dry season, and decreasing the pollutant discharge and diverted water in the lower reaches of the Minjiang River in the dry season.