The paper analyzed the temporal variation of main river discharge and the change trend of diversion ratio of Beigang by using hydrological data in downstream of Minjiang River.It used a three-dimensional environmental fluid dynamics code (EFDC) model to analyzed the effect of discharge and diversion ratio of Beigang on transport timescales (water age). The analysis result showed that annual flow of Minjiang is uneven and diversion ratio of Beigang is from small to big, then to small; there is a negative correlation between water age and river discharge. The decrease of diversion ratio will increase time of water body exchange of Beigang and will decrease that of Nangang. Water age can estimate time scales quantifying transport processes of dissolved substance for a spatially varying case. In order to protect water quality of water source areas at downstream of Minjiang, it is necessary to increase the freshwater discharge in Shuikou reservoir and the diversion ratio of Beigang during dry period.