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 (<20 μm) supporting spatial patterns of small omnivorous copepods lagoon wide (r2:0.487). A lower than expected MSP grazing pressure on phytoplankton, revealed through MSP:phytoplankton biomass ratio, however, suggested the importance of alternative food sources and foraging effects, the significance of which varied spatially. MSP–environmental interactions through gradient analysis techniques revealed unimodal functionality of MSP to contrasting horizontal explanatory gradients offered by salinity–water column transparency and nutrients–chlorophyll a. Variance partitioning revealed the importance of measured (environmental redundancy 28%; trophic gradient 32%, salinity– light gradient, 6%) and unmeasured (residual, 34%) explanatory variables contributing to the total variation in MSP within the lagoon. Overall, the superseding effects of eutrophicants on MSP dynamics coupled with cyanophycean dominance in the system suggest that this tropical lagoon is on the verge of transformation into a eutrophic/hypereutrophic system, wherein the ecological benefits achieved through the opening of a new mouth in the year 2000 appear short lived. Such changes could result in large-scale implications through trophic cascades, altering MSP dynamics and ecosystem functioning.