Estuaries are highly productive and areas of intense activity such as fishing, harbour development and aquaculture. They are also nursery grounds for many organisms. However, they are often subject to heavy human interference. Many of them receive large dosage of industrial effluents and domestic sewage. India is blessed with a large number of rivers and estuaries, but very few have received scientific attention or proper management. The case of the Cochin backwaters which has been fairly well documented point to this. Heavy industrial pollution in some areas of the estuary has caused substantial reduction of the biota. Reclamations for urban development is affecting the nursery grounds. Pollution is causing diseases to its fish fauna. Engineering follies have rendered the whole upper reaches stagnant, covered with weeds and devoid of fauna. Steps necessary to avoid such problems, protect the biota and for proper scientific management are outlined