Being one of the most vulnerable regions in the world, the Ganges-Brahmaputra-Meghna delta presents a major challenge for climate change adaptation of nearly 200 million inhabitants. It is often considered as a delta mostly exposed to sea-level rise and exacerbated by land subsidence, even if the local vertical land movement rates remain uncertain. Here, we reconstruct the water-level (WL) changes over 1968 to 2012, using an unprecedented set of 101 water-level gauges across the delta. Over the last 45 y, WL in the delta increased slightly faster (∼3 mm/y), than global mean sea level (∼2 mm/y). However, from 2005 onward, we observe an acceleration in the WL rise in the west of the delta. The interannual WL fluctuations are strongly modulated by El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) variability, with WL lower than average by 30 to 60 cm during co-occurrent El Niño and positive IOD events and higher-than-average WL, by 16 to 35 cm, during La Niña years. Using satellite altimetry and WL reconstructions, we estimate that the maximum expected rates of delta subsidence during 1993 to 2012 range from 1 to 7 mm/y. By 2100, even under a greenhouse gas emission mitigation scenario (Representative Concentration Pathway [RCP] 4.5), the subsidence could double the projected sea-level rise, making it reach 85 to 140 cm across the delta. This study provides a robust regional estimate of contemporary relative WL changes in the delta induced by continental freshwater dynamics, vertical land motion, and sea-level rise, giving a basis for developing climate mitigation strategies.