Understanding the forcing mechanisms that determine the coastal ecosystem dynamics has always been a challenging topic of research. The Arabian Sea (AS) coastal ecosystem in the western half of the northern Indian Ocean is influenced by the seasonally reversing atmospheric forcing and structured by distinct water masses along its depth. Although AS differs greatly from its eastern counter-half, Bay of Bengal (BoB) in the thermohaline characteristics, the inter-basin exchanges of the water masses between these ocean basins add complexity to its hydrography. Hence, the present study was attempted to understand the influence of the intrusion of the BoB water in structuring the zooplankton community of the coastal AS. In the mixed layer depth, a conspicuous spatial heterogeneity was noticed in the distribution and abundance of the zooplankton community contributed by the cumulative influence of the higher phytoplankton biomass and the advection of population through BoB water intrusion regulated by the coastal circulation in the southern part. The study also assessed the interaction of the zooplankton community with the specific water masses defined by distinct thermohaline characteristics along the vertical profile of the AS coastal waters. Three distinct water masses were identified within the 200 m depth of AS each categorized by discrete salinity and density features. The distinct groups of the dominant taxon, Copepoda identified through redundancy analysis demonstrate the species-specific preferences of the community to different water mass characteristics in the AS. This study addressing how hydrographic characteristics shape the macroecology of zooplankton in the coastal AS, will add new insight in understanding the dynamic ecosystems of the northern Indian Ocean.