The diversity, abundance and biomass of microzooplankton in Cochin backwaters were studied for the first time during pre – summer monsoon to peak of summer monsoon (April to July 2003) to understand the impact of large freshwater influx. Microzooplankton abundance and biomass were highest during pre – summer monsoon (av. 3817 ind. L-1 and 146 µgC L-1) that declined with the onset (av.2052 ind. L-1 and 45µg C L-1) and peak (av. 409 ind. L-1 and 10µgC L-1) summer monsoon. Species diversity, richness and evenness of microzooplankton also showed similar trends as that of abundance and biomass. Grazing experiment showed that microzooplankton consumes 43 ± 1% of the daily phytoplankton standing stock during the high saline condition (27.5). Low abundance of microzooplankton during summer monsoon period (1/9 of the pre - summer monsoon value) along with the concomitant occurrence of low mesozooplankton (1/8 times of pre summer monsoon value) suggests that there could be a general lack of planktonic grazers. This would result in a weak transfer of primary and bacterial carbon to higher trophic levels, eventually leaving behind much unconsumed basic food in the estuary during summer monsoon. Thus a major portion of the primary carbon either settles down or gets transported to the coastal regions during monsoon. High flushing of Cochin backwaters also facilitates faster removal of primary producers to the coastal regions during monsoon.