To study the relationship between sediment transportation and saltwater intrusion in the Changjiang (Yangtze) estuary, a three-dimensional numerical model for temperature, salinity, velocity field, and suspended sediment concentration was established based on the ECOMSED model. Using this model, sediment transportation in the flood season of 2005 was simulated for the Changjiang estuary. A comparison between simulated results and observation data for the tidal level, flow velocity and direction, salinity and suspended sediment concentration indicated that they were consistent in overall. Based on model verification, the simulation of saltwater intrusion and its effect on sediment in the Changjiang estuary was analyzed in detail. The saltwater intrusion in the estuary including the formation, evolution, and disappearance of saltwater wedge and the induced vertical circulation were reproduced, and the crucial impact of the wedge on cohesive and non-cohesive suspended sediment distribution and transportation were successfully simulated. The result shows that near the salinity front, the simulated concentrations of both cohesive and non-cohesive suspended sediment at the surface layer had a strong relationship with the simulated velocity, especially when considering a 1-hour lag. However, in the bottom layer, there was no obvious correlation between them, because the saltwater wedge and its inducing vertical circulation may have resuspended loose sediment on the bed, thus forming a high-concentration area near the bottom even if the velocity near the bottom was very low during the transition phase from flood to ebb. To study the relationship between sediment transportation and saltwater intrusion in the Changjiang (Yangtze) estuary, a three-dimensional numerical model for temperature, salinity, velocity field, and suspended sediment concentration was established on the ECOMSED model. Using this model, sediment transportation in the flood season of 2005 was simulated for the Changjiang estuary. A comparison among simulated results and observation data for the tidal level, flow velocity and direction, salinity and suspended sediment concentration indicated that they were consistent in overall. Based on model verification, the simulation of saltwater intrusion and its effect on sediment in the Changjiang estuary was analyzed in detail. The saltwater intrusion in the estuary including the formation, evolution, and disappearance of saltwater wedge and the induced vertical circulation were reproduced, and the crucial impact of the wedge on cohesive and non-cohesive suspended sediment distributio n and transportation were successfully simulated. The result shows that near the salinity front, the simulated concentrations of both cohesive and non-cohesive suspended sediment at the surface layer had a strong relationship with the simulated velocity, especially when considering a 1-hour lag. However, in the bottom layer, there was no obvious correlation between them, because the saltwater wedge and its inducing vertical circulation may have resuspended loose sediment on the bed, thus forming a high-concentration area near the bottom even if the velocity near the bottom was very low during the transition phase from flood to ebb.