The construction of Xingou River dredging and expanding project would affect the water quality of the Yangtze River by increasing the load of discharge. To control the risk of pollution and ensure the safety of water quality, a 2-D hydrodynamic pollutant transport model is built to examine the influence of Xingou River discharge on the water quality of Yangtze River under unfavorable conditions. Meanwhile, the background concentration of NH₃-N in Yangtze River varies remarkably in different months, hence the maximum allowable discharge is also different in different months. The results show that Xingou River discharge has apparent influence on the local water quality of Yangtze River under unfavorable conditions, and a higher NH₃-N concentration would exert greater influence. To prevent from the risk of water pollution and protect the nearby water source conservation district, the maximum allowable discharges in the presence of different background concentrations are given.