•TELEMAC-2D model was developed to assess morphodynamics in Soai Rap, Vietnam.•Mining sites were setup as specific mined volumes over time.•Dredging efficiently reduces the largest sediment deposition zone upstream.•Deposition increased substantially in the river mouth due to dredging. Recent riverbed sand mining activities have modified estuarine morphology and sedimentation patterns in many Southeast Asian deltas. The Soai Rap Estuary along the Dong Nai River (one of the largest rivers in Southern Vietnam) is one of the most intensively mined areas in the region, where large-scale sand mining activities have started since the 1990′s. In this paper, we used hydrodynamic modelling (TELEMAC-2D) to investigate the estuarine morphological changes and sediment dynamics related to the intensive riverbed mining in the Soai Rap Estuary. After the hydraulic calibration and validation of the model, we simulate four scenarios: two with dredging, one with sand excavation, and a baseline condition. Our results show that dredging substantially changed the hydraulic regimes, morphological and sediment dynamics of the estuary. Compared to the baseline, dredging substantially influences flow velocity and tidal amplitude. These activities reduce the amount of sediment accumulating upstream by 18% to 36%, while increasing sediment deposition in the Soai Rap Estuary by 6% to 13%. Furthermore, sediment accumulation in the Ganh Rai Bay area decrease by 5% to 10% due to increased sediment transport from the sea to the estuary. Our modelled results also show that the mining pits (pockmarks) created by sand extractions efficiently trap sediment, causing discontinuities in the longitudinal transport of sediment and resulting morphological patterns. We conclude that the morphology and sediment transport regime of the Soai Rap estuary has been significantly altered by the river sand dredging. As such, we recommend that the local government put in place measures to ensure that sand extraction is carried out sustainably in the future, to minimise further alterations to the natural sedimentation patterns and geomorphology of this estuary.