Coastal lagoons around the world have become increasingly vulnerable to eutrophication and often the impingement is severe with regard to plankton. In this study, we measured how environmental heterogeneity persuades mesozooplankton (MSP) community dynamics in a large tropical coastal lagoon wrought by human impingement, including the creation of a new mouth. Here, we hypothesised that trophic gradients and environmental redundancy resulting from the pooled effect of trophic and salinity– light gradients majorly influence MSP structure in one of Asia’s largest brackish water lagoons in India. Multivariate analysis of environmental variables (May 2004–September 2006; n = 1008) and MSP examined (May 2004 to October 2005; n = 522) at monthly intervals revealed discrete hydrographical and MSP regimes. Beta diversity measures revealed ∼50% community turn-over between assemblages. Residual analysis on salinity-corrected fractionated chlorophyll a and size-specific copepod functional groups revealed pico-nanoplankton (