Estuaries and coastal marine ecosystems are significantly influenced by incoming freshwater, which carries carbon, nutrients, plankton, dissolved oxygen, and suspended matter. From the perspective of ecosystem management, it is important to understand the timescales of dissolved substances taken by the water body to transport from the source to any part of the system (i.e., water age). Using the Estuarine, Coastal Ocean Model with Sediment Transport (ECOMSED), we examined the water age in a semi-enclosed bay (Lianzhou Bay) in the northern of the Beibu Gulf in China, based on the Constituent oriented Age and Residence time Theory (CART). We found that the mean age at a specific position and the runoff of the Nanliu River are well correlated and can be approximately expressed by a natural logarithmic function. The water age is strongly affected by the river runoff and tides.