Zooplankton communities in response to hydrological (salinity, turbidity, water temperature, nitrate, phosphate, silicate) and biological (phytoplankton density) variables were studied in the Asia’s largest brackish water lagoon, Chilika (India). Water samples were collected from 13 stations on a monthly frequency between July 2014–June 2015. A total of 141 species of holoplankton including Ciliophora, Foraminifera, Rotifera, Rhizopoda, Gastropoda, Cladocera, Copepoda, Ostracoda, Malacostraca, Chaetognatha, Chordata, Nematoda, and 18 types of planktonic larvae were identified. Copepods were the most dominant and diverse zooplankton in terms of their species richness, numerical abundance, and widespread distribution in the lagoon. The major holoplanktonic taxa were Acartia sp., Acrocalanus gibber, Acrocalanus gracilis, Acrocalanus longicornis, Euterpina acutifrons, Lecane sp., Oithona sp., Pseudodiaptomus serricaudatus, and Tintinnopsis tubulosa. The dominant planktonic larvae were bivalve veliger, copepod nauplii, cyphonautes larvae, gastropod veliger, and protozoea of lucifer. Canonical correspondence analysis showed that distribution of zooplankton assemblages was influenced by salinity, turbidity, and phytoplankton density. Indicator analysis demarcated 26 indicator zooplankton taxa. Of these, the most prominent indicator zooplankton such as Belzebub hanseni, Mesopodopsis orientalis, Chydorus sphaericus, and Corycaeus catus were characteristic to salinity gradient in southern sector, sediment resuspension in central sector, eutrophic conditions in northern sector, and intrusion of inshore forms in outer channel, respectively. Hudhud, a category 4 cyclone resulted decline in the abundances of zooplankton population. Copepod nauplii and copepodites were dominant during post-Hudhud and their succession was linked to the increased phytoplankton density due to an upsurge in the nutrient level in the northern sector of the lagoon. The present study provided a comprehensive detail on the zooplankton composition and their environmental drivers including the impact of a tropical cyclone from a tropical coastal lagoon system.