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This research aims to investigate the prevailing sediment dynamics and the sediment budget in the Mekong Delta by using a process-based model. Understanding sediment dynamics for the Mekong Delta requires high resolution analysis and detailed data, which is a challenge for managers and scientists. This study introduces such an approach and focuses on modeling the entire system with a process-based approach with Delft3D-4 and Delft3D Flexible Mesh (DFM). The first model is used to explore sediment dynamics at the coastal zone. The latter model allows straightforward coupling of 1D and 2D grids, making it suitable for analyzing the complex river and canal network of the Mekong Delta. The validated model suggests that the Mekong Delta receives 99 Mt/year sediment from the Mekong River. This is much lower than the common estimate of 160 Mt/year. Only about 23% of the modelled total sediment load at Kratie is exported to the sea. The remaining portion is trapped in the rivers and floodplains of the Mekong Delta. The results advance understanding of sediment dynamics and sediment budget in the Mekong Delta. As such the model is an efficient tool to support delta management and planning.