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Tropical monsoonal estuaries have a significant role in global fishery as they act as rich feeding and breeding grounds for many commercial species. Food web dynamic studies in these coastal ecosystems are mainly focused on the classic food chain which assumes that microbial food webs contribute more towards the recycling of organic carbon and nutrients rather than production. But recently it is observed that phyto-microbial food web which is largely dependent on pico-autotrophs can contribute significantly towards the higher trophic level. Based on these observations we have analysed phyto-microbial pathway of food web in a highly productive tropical monsoonal estuary. We assessed the grazer-prey interaction in the microbial food web of Cochin estuary during spring intermonsoon and southwest monsoon seasons. Our results show that during spring intermonsoon the food web is dependent more on heterotrophic bacteria, but in southwest monsoon the dependency of grazers switches over to autotrophic picoplankton. We also analysed the growth rate, grazing rate and carbon contribution of autotrophic picoplankton experimentally during both seasons and found that autotrophic picoplankton show higher growth rate during southwest monsoon. The higher grazing rate and clearance rate of autotrophic picoplankton recorded during southwest monsoon indicate the efficient consumption of autotrophic picoplankton crop during the season. We could also observe a change in autotrophic picoplankton community structure between the seasons with the dominance of picocyanobacteria during spring intermonsoon and that of picoeukaryotes during southwest monsoon. Thus we infer that high freshwater influx into the estuary during monsoon results in high turbid and low saline (mesohaline to oligohaline) environment which increases the growth rate of low light adapted autotrophic picoplankton populations and in turn enhances herbivory (phyto-microbial pathway) in the microbial food web. Apart from protists, autotrophic picoplankton were found to be widely consumed by many larval forms of mesozooplankton, gastropods, bivalves, rotifers and large sized filter feeders either as aggregates or as unicellular forms. Thus monsoon enhanced herbivory can have a significant role in the growth and survival of larval forms recruited into the estuary during monsoon season and in turn the fishery. • Salinity reduction associated with monsoon enhances herbivory in the pelagic microbial food web of the estuaries. • Enhanced herbivory can have a significant role in the growth and survival of larval forms recruited to the estuaries. • Classic food chain concept is mainly based on the carbon contribution of large phytoplankton. • Autotrophic picoplankton and picoeukaryotes may also contribute to the fishery production of the tropical coastal ecosystems. [ABSTRACT FROM AUTHOR]