Sundaland is the currently partially drowned continental landmass that encompasses Borneo, Sumatra, Java, and the Malay Peninsula. It has episodically been reclaimed by the sea during successive Quaternary glaciations, and is commonly thought to be vertically stable. Combining geomorphological observations with numerical simulations of coral reef growth and shallow seismic stratigraphy, we show that the Sunda shelf is subsiding, and that the intermittent regime of transgressions only prevailed over the past 400,000 yr. Prior to that time, Sundaland was permanently exposed. We relate these drowning events to transient dynamic topography in the Indo-Australian subduction zone. Because the Sunda shelf is very shallow, these new data provide important insights into Pleistocene paleogeography, with implications on the interactions between the solid Earth and climate, oceanography, and dispersal of species, including hominids.