The discharge of fertilizers and untreated sewage from the Indian subcontinent was attributed to damage the coastal ecosystem and threat to the fishery resources. Based on the recent data collected along the Indian coasts, the issues were reanalyzed to identify potential mechanisms responsible. Carbon, nitrogen and oxygen isotopes revealed that the fertilizers used in the agricultural soil contaminate groundwaters, then fluxed to the coastal ocean. Similarly, the impact of municipal sewage is restricted close to the coast rather than spreading to the international waters. This reanalysis suggests that the occurrence of coastal eutrophication, hypoxia or shift in the ecosystem was mainly caused by natural processes such as coastal upwelling, stratification and reversing of coastal currents than hitherto hypothesized as the discharge of fertilizers and municipal sewage.