The concept of water age is applied to calculate the timescales of the transport processes of freshwater in Lianzhou Bay, using a model based on ECOMSED. In this study, water age is defined as the time that has elapsed since the water parcel enters the Nanliu River. The results show that the mean age at a specified position and the runoff of the Nanliu River are well correlated and can be approximately expressed by a natural logarithmic function. During the neap tide, it takes 70, 60 and 40 days in the dry, normal and rainy seasons for water to travel from the mouth of the Nanliu River to the northeast of Lianzhou Bay, respectively, which is not beneficial to water exchange in the bay. Tides significantly influence the model results; it takes five less days for the tracer to be transported from the mouth of the Nanliu River to the north of Guantouling during the spring tide than during the neap tide.