The Maldive archipelago consists of 22 main atolls characterized by a marginal rim surrounding a lagoon commonly less than 50-60 m deep, though some lagoons reach depths of more than 80 m in the South. The overall evolution of the carbonate system in the Maldive Archipelago clearly shows that the slow subsidence of hypothetical volcanic edifices buried under the atolls cannot explain their typical ringed morphology. Our research in the Maldives was developed based upon the interpretation of two Elf-Aquitaine and Royal Dutch Shell MCS grids, groundtruthed by two deep exploration wells and ODP Site 716. Several seismic profiles across the modern atoll margins clearly illustrate a shift from middle Miocene-early Pliocene sigmoid lateral margin progradation of flat-topped carbonate banks to late Pliocene-Quaternary bank top vertical aggradation evolving into the modern atoll physiography. This well-marked transition is first illustrated by a regionally observed downward shift of the depositional system dated at 3.0-2.5 Ma. This downward shift of onlap is explained by a late Pliocene-early Pleistocene overall sea level regression tied to the onset and successive expansions of major continental ice sheets in the northern Hemisphere. The early Pliocene bank-tops remained exposed for about 2 My, prior to being successively flooded and exposed by a series of five, 120 m high amplitude, late Brunhes sea level transgressions and regressions. Bank top karst topography, enhanced during the series of exposures, became the substratum for reef development during the intervening sea level transgressions and, therefore, explained the modern atoll physiography observed in the Maldive Archipelago.