The distribution and composition of zooplankton are influenced by a combination of physico-chemical and biological processes, which in turn have effects on the entire ecosystem. In this study, the influence of environmental factors on zooplankton diversity in mangrove-estuarine coastal waters of Parangipettai, southeast coast of India, was investigated. Water samples were collected for a period of four years from January 2014 to December 2017. Totally, 145 species of zooplankton were recorded with highest belonging to the Arthropoda (63.21%) followed by Protozoa (10.53%), Cnidaria (7.95%), Urochordata (6.03%), Chordata (2.92%), Chaetognatha (2.62%), Mollusca (2.42%), Echinodermata (1.14%), Annelida (1.05%), Brachiopoda (1.01%), Ctenophora (0.57%) and Phoronida (0.55%). The findings of cluster, MDS, Factor analysis and CCA showed that variations in nutrient concentration may significantly alter the biotic community of zooplankton species. Furthermore, site score confirmed the effect of environmental conditions on zooplankton distribution. The result of TRIX showed the dry seasons are classified as scarcely eutrophied whereas wet seasons as moderately eutrophied. The findings of this study offer enhanced insight into how physico-chemical factors interact and vary over space and time, which is crucial for evaluating the effects of climate change on ecosystem services mediated by zooplankton.