Abstract: In order to study the hydrodynamic characteristics of saltwater intrusion in the Modaomen waterway, a three dimensional baroclinic numerical model with large scale and high-resolution grids, covering the entire upstream river network, the Pearl River estuary and its adjacent sea, was set up based on the Finite Volume Coastal Ocean Model (FVCOM) and then validated and calibrated against measured data. Numerical experiment of saltwater intrusion in the Modaomen waterway was carried out with this model. According to simulated results and measured data, the mechanisms of stratification, mixing and salt transportation during spring, moderate and neap tide were analyzed. Results show that the salt transportation in the Modaomen waterway is dominated by bottom high-salinity water and its net mass is landward during neap tide. However, it is dominated by surface low-salinity water and the net mass is seaward during flood tide. The balance of salt transportation will appear within moderate tide. As a result, the saltwater intrusion in the Modaomen waterway reaches its peak and nadir during the coming moderate tide after neap and flood tide respectively.