Severe floods usually result in harmful sediment and pollutant dispersion in shallow coastal regions. This study therefore presents a three-dimensional hydrodynamic and transport model investigation into the sediment transport behaviour following severe flooding which occurred in the Brisbane River catchment. It was found that the flood-driven sediment plume formed in the adjacent Moreton Bay and then spread into the northern part of the bay. Based on analysis of the variations in horizontal sediment flux, four distinct characteristics of sediment transport were identified, corresponding to the combined effects of flooding runoff and tidal currents. Firstly, within the estuary, sediment was driven by the flood discharge and primarily transported in the seaward direction. Secondly, at the river mouth, the transport pattern of the sediment was similar that of the first region, however, the horizontal flux was significantly smaller by 50%. Thirdly, a short distance from the river mouth, variations occurred not only in magnitude but also in transport pattern. Lastly, within the coastal bay, the sediment transport was mainly driven by tides, resulting in the changing direction of sediment movement. It was estimated that approximately 1.01 × 106 tonnes was discharged from the Brisbane River estuary into the bay during the flood event in January 2011. This study exhibited the characteristics of sediment transport within a tidal dominant estuary following a severe flood event. The results would be used to assist the implementation of coastal management strategies.