The dynamics of Northeastern Arabian Sea (NEAS) is governed by convective mixing in winter and stratification during the inter-monsoon spring seasons, wherein blooms of green Noctiluca scintillans is a recurrent phenomenon. The study investigated the role of microzooplankton (MZP) in mediating the microbial food web in bloom waters of Noctiluca scintillans. The winter monsoon and inter-monsoon spring periods for the years 2009, 2011 and 2012 were considered for the present study as the occurrence and intensity of bloom fluctuates between these seasons. The MZP mediation seems to be through the top-down controls (preferential grazing) on ciliates (CTS) in bloom waters, consequently supporting high mesozooplankton standing stock and inevitably higher stock of copepods. Among the three years of observations, this relation was noticeable for the year 2012, as the intense bloom of Noctiluca (3 ×107 cells L−1) coincided with the highest number of copepods. On the contrary, in the non-bloom waters, a simple classical food web seems to be operational as diatoms dominated the phytoplankton community. Furthermore, the functional role of two CTS species viz. Codonellospsis ecaudata and Steenosemella ventricosa were most influential in structuring the community and microbial food web in the bloom events. The study suggests that during the bloom of Noctiluca scintillans, MZP mediated food web seems to be relatively significant in sustaining the high secondary production in the NEAS.