Relative sea level history, which is the result of the combined effects of land subsidence, sediment supply and absolute sea level history may be reconstructed from preserved sediment thicknesses. However, variations in the preserved sediment thicknesses between different sedimentary environments strongly limit the accuracy of this type of geological approach, particularly in fluvial channelized systems, such as delta plains. To address this, we apply three different and independent stratigraphic approaches to the case of the Ganges–Brahmaputra–Meghna Delta (GBMD). Our approach has been made possible by a broad dataset of geological archives we have collected, which includes more than 400 hand-drilled stratigraphic wells, 198 radiocarbon ages, and river seismic reflection data (255 km of high-resolution multichannel seismic images). The seaward gradient of accommodation and the limit of the subsiding delta plain are estimated, assuming that the delta is near or at the base-level, which is considered to be the relative sea-level. First, a statistical analysis of the variability of preserved sediment thicknesses is used to derive the average pattern of accommodation from the Holocene isopach. Secondly, the preserved sediment thicknesses are analyzed by geomorphotectonic domains to estimate an average pattern of accommodation. Thirdly, the burial history of the seismically imaged last glacial incision of the Brahmaputra River is reconstructed. Results suggest that the variability of preserved sediment thicknesses can be up to 35% in a delta plain between river channel and flood plain deposits for the same relative sea-level history. Taking this variability into consideration, the Holocene relative sea-level history of the GBMD and the most likely pattern of subsidence are determined. Results provide evidence of moderate Holocene subsidence over the delta, gently increasing seaward from <0.2 mm/yr landward of the Hinge Zone, which can be considered as the northern limit of the subsiding delta plain, to 2 ± 0.7 mm/yr in the middle fluvial delta to 4 ± 1.4 mm/yr in the lower tidal delta. This enables us to construct the first millennial-scale map of subsidence pattern on the GBMD in which uncertainties on subsidence rates are provided. This map may aid in evaluating the negative impact that human modification may have on subsidence and relative sea level in the GBMD, and thereby help to determine better sustainable coastal management practices for the GBMD and other large delta plains.