Coastal waters are dynamic because of anthropogenic activities that contribute nutrients and contaminants. These changes have the potential to alter patterns of primary production and thus pelagic food webs. Here, we investigated the spatial variation of the phytoplankton community and its response to changing environmental variables at 84 stations along the five coastal districts of Tamil Nadu (TN). During the present study, 85 phytoplankton species were recorded, such as diatoms (64), dinoflagellates (18), silicoflagellates (1), and Cyanophyceae (2). The maximum phytoplankton abundance was recorded on the Thanjavur coast and gradually decreased towards the south coast of Tamil Nadu. Among the phytoplankton community, 50% was dominated by pennate diatoms, attributed to higher NO3− concentrations in the coastal waters due to agricultural discharge. Cluster analysis revealed that Ramanathapuram and Tirunelveli formed a closed cluster, whereas Thanjavur and Pudukottai formed a separate closed cluster associated with higher nutrient and metal concentrations, highlighting the difference in physicochemical parameters between the northern and southern districts of the TN coast. Relatively high nutrient concentrations in the coastal waters of northern districts are of greater concern, which could impact the coastal ecosystem. Coastal eutrophication is becoming a widespread phenomenon, causing disruption in the food chain and ecosystem balances and hence requiring regular monitoring and management.