A survey along the coast of India (~1100 km stretch) between Benaulim (Goa) in the west coast and Thoothukudi (Tamil Nadu) in the east coast was conducted during summer 2014, to evaluate the mesozooplankton community structure. Zooplankton community was dominated by holoplanktonic forms representing 93.7% of the total zooplankton, while meroplanktonic forms constituted 6.3%. Zooplankton was generally dominated by copepods which contributed about 69%. In total, forty-eight species of copepods belonging to eighteen families dominated the zooplankton abundance, with a significant contribution of small-sized copepod genera, viz. Bestiolina, Parvocalanus, Acrocalanus, Corycaeus, Oncaea and Oithona. Total mesozooplankton and copepod density ranged from 80 ind. m−3 to 804 ind. m−3 and 28 ind. m−3 to 570 ind. m−3, respectively. Considerably higher abundance of cladocerans (Penilia avirostris and Evadne tergestina) with a significant contribution to zooplankton biomass (r2 = 0.984, p < 0.01) compared to copepods was recorded along the east coast. The results of RDA analysis revealed that the sea surface temperature (SST), nutrients (SiO4 and NO2), dissolved oxygen (DO) and total suspended matter (TSM) were significant environmental variables (p < 0.05; 999 Monte Carlo permutations) associated with the community structure during pre-monsoon period. Both copepod diversity (H′) and dominance (λ) index were higher along the west coast, suggesting the influence of high nutrient and organic input from riverine influx coupled with complex environmental features. The inverse relationship between chlorophyll-a and copepod diversity (H′: r = −0.488, p < 0.01) substantiated the importance of grazing pressure in these coastal waters. In contrast, a positive relationship between chlorophyll-a and copepod dominance (λ: r = 0.434, p < 0.05) indicated that copepods abstained from grazing on phytoplankton. Further characterization of this variability in community structure along the coastal waters requires long-term monitoring at a lower taxonomic level