The estuary is the transition zone between the riverine and marine environments, in which the zooplankton act as a trophic connector in the energy transfers from primary producers to secondary consumers. Zooplankton biovolume and species assemblages with reference to physical, chemical and biological properties in the Indian estuaries are rarely studied. To examine the zooplankton variability in abundance and diversity, we therefore, investigated seventeen Indian estuaries during the post monsoon of the year 2012. Based on salinity conditions, estuaries were classified into oligohaline, mesohaline and polyhaline. A marked spatial gradient in salinity was observed between the upstream and downstream estuaries. Relatively, salinity was high in downstream areas, resulting in high zooplankton biovolume and diversity perceived in downstream areas. In contrast, nutrient concentrations were higher in the upstream than the downstream estuaries, resulting in high phytoplankton biomass (in terms of chlorophyll-a) perceived in the upstream estuaries. Zooplankton abundance was numerically dominated by Copepoda, constituting approximately 76 % of the total zooplankton count. Zooplankton population was highly similar between upstream and downstream in the oligohaline estuaries. In contrast, heterogeneous assemblages were noticed between upstream and downstream in the mesohaline and polyhaline estuaries. Under oligohaline conditions, surface waters dominated by Acartia clausi, A. dane, A. plumosa, Cyclopina longicornis, Oithona rigida and Tigriopus sp. In contrast, under mesohaline and polyhaline conditions, Acartia tonsa, Acartia southwelli, Acartia spinicauda, Paracalanus spp. Centropages typicus, Temora turbinate, Oithona spinirostris and O. brevicornis become the key dominant species. Eucalanus spp., and Corycaeus spp. were indicator species in the downstream estuaries. Our findings suggest that zooplankton diversity and numerical abundance were chiefly governed by salinity rather than phytoplankton biomass (chlorophyll-a) in the Indian estuaries during the post monsoon.