The subsidence of the Ganges‐Brahmaputra‐Meghna Delta (GBMD) drastically increases the adverse impacts of coastal flooding and exacerbates the vulnerability of populations from ongoing rapid sea level rise. We focus here on estimating the present‐day subsidence rates induced by the loading of sediments continuously deposited within the GBMD over the past 11,000 years. By constructing a realistic GBMD 3‐D numerical model with laterally variable mantle and lithospheric structure, we demonstrate for the first time that the presence of the strong Indian Craton and the weakened Indo‐Burma margin results in significant amplification of subsidence driven by sediment loading in the eastern part of the delta, where the population density is the highest (>1,000 habitants per km²). Although uncertainties remain regarding the amplitude of subsidence, the rate estimates (2–3 mm/year) are found to be comparable to the present‐day global mean sea level rise.