The hydrological process dominates the spatial and temporal concentrations of nutrients and other biogeochemical compounds in the large estuary where river and ocean meet. Water age is a measure of water renewal timescale and a characteristic parameter of hydrodynamics and contaminant transport. A large-scale river-sea linked and multi-process coupled 2D EFDC model was constructed from Datong hydrometric station of Changjiang River to the East China Sea. The effects of changes in river discharge on hydrodynamics and nutrients in the Changjiang Estuary were simulated and analyzed. Pollutant loads to the Changjiang Estuary are mainly from upstream inflows and local inputs. The proportion of total phosphorus (TP) loads from upstream is greater than the total nitrogen (TN) loads, accounting for about 90% and 78%, respectively. As the river discharge decreases, TN concentrations decrease in most regions, except for near large sewage discharges where TN concentrations increase while TP concentrations show a decreasing trend. When the river flow drops from over 60000 m3/s to a relatively low value of 10000 m3/s, the average TN concentration in the southern channel of the Shanghai section of the Changjiang Estuary increases by nearly 13%, while TP concentration decreases by nearly 5%. The model results show that the water age inside the river mouth is inversely proportional to the flow rate. In contrast, the water age outside the mouth is negatively with the river discharge. The water age maximum zones (WAMZ) are found in the estuary, ranging from within the estuary to 90 km from the mouth, and are likely to coincide with the positions of the turbidity maximum zones (TMZ), which move seawards or landwards with the increase or decrease of river discharge in the Changjiang Estuary. In addition to location, the value of water age maxima varies negatively with river discharge, which is also relevant to turbidity intensity likely. Water age and WAMZ can be the indicators to predict the changes in the water environment and nutrient sinks in the Changjiang Estuary.