Consequences of a catastrophic flood on the habitat quality and the concurrent responses of the bentho-pelagic community were studied in Cochin estuary, a eutrophic estuary along the southwest coast of India. The episodic flood in 2018 led to a marked decline in the dissolved nutrients and heavy metal concentrations in water and sediments of the estuary. The pre-flood phytoplankton abundance dominated by a bloom-forming species Cerataulina bicornis experienced a significant drop after the flood. Contrarily, zooplankton and macrobenthos responded favorably towards the flood-imposed habitat alterations. Higher susceptibility to heavy metal pollution and increased grazing pressure from gelatinous carnivores restricted the abundance of Copepoda, the dominant zooplankton taxon during pre-flood. The lower heavy metal concentration in the sediment after the flood favored higher macrobenthic abundance and diversity with a conspicuous change in the community structure from opportunistic polychaetes, indicators of pollution to molluscans and crustaceans, indicators of the healthy benthic zones.