The growing number of oxygen-deficient coastal zones around the world and their impacts on marine life has always been a controversial issue as their development is largely attributed to anthropogenic activities which can be mitigated by human actions. However, contrary to this prevailing understanding, we show here for the first time, using new coherent datasets from estuaries to coastal to offshore regions, that the world's largest hypoxic-anoxic zone along the west coast of India is formed through a natural process, i.e. upwelling of deoxygenated waters during the summer monsoon. We further demonstrate that the persistence and extent of this coastal oxygen deficiency depend on the degree of deoxygenation of source waters for the upwelling. Consequently, the anoxia is confined only to the central shelf between 11° and 18° N, which is equivalent to almost half of the western Indian shelf, where upwelling brings suboxic waters from the core oxygen minimum zone in the Arabian Sea.