As a multi-branch estuary system, the Yangtze Estuary presents distinctive characteristics of hydrodynamic processes through co-action among river runoff, tides, wind-waves, and gravitational circulation. To study the pathways of flushing water along all of the estuary’s branches and analyze their differences, especially those due to the influence of seawater intrusion and discharge variations, a free surface flow modeling suite TELEMAC-MASCARET involving passive tracers was applied to the Yangtze Estuary and the adjacent waters. The open boundary conditions were provided by the Nao.99b model (Matsumoto et al., 2000), which was calibrated using observed velocity and salinity data obtained in March 2002. The water age, which was used as the diagnostic tool to study the flushing efficiency of the water body across the estuary, was solved by additional advection-diffusion-reaction equations implemented in the TELEMAC modeling system. The transport properties were investigated under different river discharge scenarios, which represented seasonal impacts; aspects relating to the influence of tide, surface wind stress, and density-induced circulation on age were also investigated. Model results showed that river runoff is one of the dominant factors influencing the spatial distribution of the mean age, while tidal force is another important factor. The horizontal freshwater age distribution demonstrated similarity compared with the salinity distribution; the vertical age distribution resembled the stratification pattern of salinity in all branches where stratification persists. An experimental numerical simulation of tracing saltwater age from the lower reaches of the estuary was conducted, and implicated the connectivity with transport processes of freshwater from upstream. Additionally, a particle tracking algorithm was used to analyze the dynamic characteristics of the four passages. The South Passage and South Channel were found to be significant as main water flow passages, while salinity intrusion in the North Branch was found to cause a return flow that partially joins the South Branch flushing water.