The diversity of macro and meiobenthos was documented in order to assess the ecosystem health of an anthropogenically impacted coastal ecosystem for the first time along the southwest coast of Tamil Nadu. Offshore sediment and water samples (n = 63) were collected from 14 sampling stations using the grid sampling method. Water and sediment samples were analysed for environmental variables such as pH, temperature, electrical conductivity (EC), total dissolved solids (TDS), salinity, sulphate, dissolved oxygen (DO), carbohydrate (CHO), protein, lipid, labile organic matter (LOM), total organic carbon (Corg), total organic matter (TOM) and sediment texture using standard methods. Benthic macro and meiobenthos were isolated and identified using standard identification keys. A total of 5 phyla of macrobenthos with 29 species and 5 phyla of benthos with 60 species were identified in the study area. Relative abundance analysis showed that the largest numbers of species belonged to Polychaeta for macrobenthos and foraminifera for meiobenthos. Redundancy analysis indicated that sediment carbohydrate content was the highest determining factor for explaining variation in the diversity of benthos. AMBI & M-AMBI results revealed that among the 14 stations, 2 were categorized as “poor” and 9 as “bad”. Multiple anthropogenic activities in the coastal environment leading to increased organic matter input have resulted in a decline in the ecosystem health of this region, which warrants site-specific management to control organic pollution.