Geologically, the Sunda Shelf is an extension of the continental shelf of Southeast Asia, covered during interglacials by the South China Sea, which isolates as islands Borneo, Sumatra Java and smaller islands. During Glacial periods, the sea level falls, and great expanses of the Sunda Shelf are exposed as a marshy plain. The seas and bays that cover the Sunda Shelf are less than 100 m deep.

Steep undersea gradients separate the Sunda Shelf from the Philippines, Sulawesi and the Lesser Sunda Islands, where the dividing line, passing between Bali and Lombok, is marked by a major discontinuity in fauna that is known as the Wallace Line from Alfred Russel Wallace, the biologist who first recognized it in the 19th century.