The Pearl River, one of the seven largest rivers in China, drains into the South China Sea. To simulate the transport and distribution of non-saturated suspended sediments in the Pearl River Estuary, a three-dimensional sediment transport model coupled with a three-dimensional hydrodynamic model has been developed. The model was validated by comparing simulation results with suspended sediment concentrations measured on July 25–26, 1999 at four sites within the study area. The validation indicated that the model can simulate the transport and distribution of suspended sediments reasonably well. The simulated surface suspended sediment concentrations matched the satellite images qualitatively. It was found that suspended sediments in the study area exhibit strong vertical stratification, and sediment concentrations near the river gates are generally lower in the surface layer of the water column and increase with water depth while the minimum concentrations may be observed in the middle layer of water column where fresh and salt waters meet together. Generally, suspended sediments discharged from each river gate are carried by currents along the coast toward the southwest. During both high- and low-tide periods, the horizontal distribution of suspended sediment concentrations clearly demonstrates peaks adjacent to the river gates and a spatially decreasing trend from the northwest to the southeast in the study area. Contours of suspended sediment concentrations often migrate toward the ocean at low tides outside of most river gates. All these findings indicate that suspended sediments in the Pearl River Estuary primarily have terrestrial sources.