The three-dimensional circulation, salinity distribution, and overall transport pattern were simulated in the Pearl River Estuary, China, using a modified version of the Princeton Ocean Model (POM). The circulation in the estuary is mainly driven by tide, wind, and river runoff in a complex manner, where the relative importance of the different forcing factors varies over the year. Field data on currents from several locations in the estuary taken at different elevations through the water column were employed to validate the model together with measurements of the salinity distribution in the surface layer. Also, satellite images were utilized to qualitatively confirm the simulated overall transport pattern. Comparisons between measurements and calculations showed that the POM yielded satisfactory predictions without any particular calibration. However, for some events the coastal current outside the estuary induced by the large-scale circulation in the South China Sea affected the flow in the estuary, making it necessary to employ a more sophisticated boundary condition on the ocean side than what was initially implemented. The long-term objective of the numerical modeling of the flow and material transport in the Pearl River Estuary is to utilize the validated model for forecasting the circulation and water quality in the estuary in a comprehensive system where in-situ measurements and remote sensing are the other main components.