A process-based model for the Yangtze Estuary is constructed to study the sediment transport in the estuary. The proposed model covers the entire tidal region of the estuary, the Hangzhou Bay and a large part of the adjacent sea. The dominant processes, fluvial and tidal, are included in the model. The calibration of the model against extensive flow, water level, salinity and suspended sediment data shows a good representation of observed phenomena. With the present calibrated and validated model, the residual flow field and the residual sediment transport field are obtained. The residual sediment transport pattern gives insight into the morphological behaviour of the mouth bars.