Fluvial sediment supply towards the coast has been the subject of extensive research. Important aspects relate to the impact of sediment retaining hydropower dams, potential delta progradation, coastal sediment supply and delta vulnerability to sea level rise. Once validated, process-based models provide a valuable tool to address these aspects and offer detailed information on sediment pathways, distribution and budget in specific systems. This study aims to advance the understanding of the sediment dynamics and sediment budget in the Mekong Delta system. We developed a process-based model (Delft3D FM) that allows for coupling 2D area grids to 1D network grids. The flexible mesh describes both wide river sections and channel irrigation and drainage networks present in the Mekong Delta. We calibrated the model against observed discharge, salinity, suspended sediment concentration (SSC) and sediment flux. The model was able to skillfully describe seasonal variations of SSC and hysteresis of SSC and water discharge caused by the Tonle Sap Lake induced flow patterns and seasonally varying bed sediment availability in the channels. Model results suggest that the Mekong River delivers an amount of sediment, towards the delta which is much lower than the common estimate of 160 Mt/year. About 23% of the modeled total sediment load at Kratie reaches the sea. Our modeling approach is a useful tool to assess sediment dynamics under strategic anthropogenic interventions or climate change scenarios.