Abstract: Water transport process is the basic condition of pollutants transformation, the flowing velocity of the process has a significant influence on water exchange and pollutants degradation. Based on the water age and Lagrangian particle tracer module of Environmental Fluid Dynamic Code (EFDC), we analyzed the effect of upstream Yangtze River runoff on water transport in Jiangsu reach under different designed discharge and specific lower boundary tide level. The specific study reaches was from Nanjing to Xuliujing, where the surrounding economy is well developed and pollution load discharge is large. The results showed that the transport time was slower in the lower reaches due to the effect of tide and much more significant influence by discharge under the small flow. Comparing the transport time given by the two calculating methods, the Lagrangian particle tracer method is much more stable because the water age method can be influenced by downstream open boundary condition. The relationship between the transport time and runoff along the flow path could be calculated by quadratic function. The relationship between the transport time of the water flow reaching the inlet to or completely passing through the specific site and the water age of the corresponding site can be calculated by the power function, and both the fitting effects were very good. The numerical model simulation method can reflect and characterize the water transport characteristic in the study area. This study can increase our understanding of the process of material transport in tidal rivers, and provide new ideas for early warning and management measures of sudden polluted accidents in rivers.