Cochin backwaters, a micro tidal estuary, undergo a characteristic transformation from a river dominated system during summer monsoon to a tide-dominant system during pre-monsoon season. The present study observes that as the river flow weakens after monsoon, the flushing of the estuary diminishes and the nitrogen and phosphorous loadings through anthropogenic activities (industries) and sediment re-suspension alter the nutrient stoichiometry substantially. The increased tidal activity during pre-monsoon changes the estuary into a vertically mixed, eutrophic and flow-restricted system supporting an enhanced organic production. This implies that monsoon-induced hydrology plays an important role in regulating the nutrients, secondary production and even the migrant fauna of the estuary. The system is delicately poised, as continuous release of pollutants including nutrients into this estuary would suppress fish and shellfish production, where only pollution tolerant species can exist.