Deltas are low-lying plains which are formed when river sediments deposit in coastal environments. Deltas are nutrient-rich, and productive ecological and agricultural areas with high socio-economic importance. Globally, deltas are home to about 500 million people and are considerably modified by human activities. In addition, they are vulnerable to climate change and natural hazards like changing river flow and sediment supply, coastal flooding by storminess or sea level rise. To encourage better delta management and planning, it is of utmost importance to understand existing delta sediment dynamics. The objective of this study is 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, 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 analysing the complex river and canal network of the Mekong Delta. This study starts by generating trustworthy bathymetries based on limited data availability. It describes a new interpolation method for reproducing the main meandering channel topographies of the Mekong River. The reproduced topographies are validated against high resolution measured data. The proposed method is capable of reproducing the thalweg accurately. Next, this study describes the development of a Delft3D Mekong Delta model. The model is validated for hydrodynamics and sediment dynamics data for several years and focuses on describing near shore sediment dynamics. The model shows that sediment transport changes in the Mekong Delta are strongly modulated by seasonally varying river discharges and monsoons. The nearshore suspended sediment concentration (SSC) is significantly decreased due to a lack of wave-induced stirring when there is no monsoon. 3D Gravitational circulation effects limit the SSC field from expanding seaward in case of high river flow. In addition, the bed composition has an important role in reproducing sediment fluxes which were considerably decreased when a sandy bed layer is included. This happens due to effects of the initially mostly sandy mixing layer, where resuspension of the mud is proportional to the fraction of mud present. It takes time for an equilibrium bed composition to develop. Seasonally, the sediment volumes deposited in the river mouths increase regularly during the high flow season. During October they remain more or less constant and then, as wave action increases and discharges decrease, the deposited material is resuspended and transported southward along the coast. The DFM model explores the hydrodynamics and sediment dynamics in the fluvial reach of the Mekong River including the anthropogenic effect of dyke construction. After an extremely high flood in 2000 which caused huge damages, a dyke system has been built to protect agriculture in the Vietnamese Mekong Delta (VMD). These structures change hydrodynamic characteristics on floodplains by avoiding floodwaters coming into the floodplains. The DFM model shows that the high dykes slightly change hydrodynamics in the VMD downstream. These structures increase daily mean water levels and tidal amplitudes along the mainstreams. Interestingly, the floodplains protected by high dykes in Long Xuyen Quadrangle and Plain of Reeds influence water regimes not only on the directly linked Mekong branch, but also on other branches. Based on the validated hydrodynamic model, the model is validated against sediment data and used to derive a sediment budget for the Mekong Delta. For the first time, this study has computed sediment dynamics over the entire Mekong Delta, considering riverbed sediment exchange. The 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. Located between Kratie and the entrance of the Mekong Delta, the Tonle Sap Lake receives Mekong River flow at increasing flow rates seasonally and returns flow when Mekong River flow rates decay. As a result Tonle Sap Lake traps approximately 3.9 Mt/year of sediments and explains the hysteresis relationship between water discharges and SSC at downstream stations. The VMD receives an amount of 79.1 Mt/year (~80 % of the total sediment supply at Kratie) through the Song Tien, the Song Hau and overflows. The model results suggest that the Mekong mainstream riverbed erodes in Cambodia and accretes in Vietnam. The results of this study advance understanding of sediment dynamics and sediment budget in the Mekong Delta. The model developed is an efficient tool in order to support delta management and planning. The validated model can be used in future studies to explore impact of climate change and human interference in the Mekong Delta.