The Ganges-Brahmaputra-Meghna (GBM) Delta is a good example of a large estuarine system with sparse data. This study describes the development and validation of a morphodynamic process-based model (Delft3D) as a tool to predict the dynamic system as a response to climate change, sea-level rise, subsidence and other influences. The modelled sediment transport of the Ganges and Jamuna systems is between 200 and 1100 million ton/year, which is in line with observations. On annual basis sand accounts for less than 20% of the sediment load in the system with the remaining sediment being much finer. Analysis of modelled bed level changes over time reveals that only a few river systems are in an aggrading phase. The 2D model exhibits that about 22% of the supplied sediment deposits in the delta system on floodplains and tidal plains, whereas the remaining 78% of the sediment causes subaquatic delta progradation or is lost in the deep ocean bed. Although the model does not reproduce all-natural phenomena at all spatial scales, it will be a valuable tool to describe and explore the morphodynamic development of the GBM Delta over decadal to centennial timescales for macro-scale understanding, planning, and management.