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Marine pollution poses significant risks to both human and marine health. This investigation explores the limnological status of the Odisha and West Bengal coasts during the annual cruise program, focusing on the influence of riverine inputs on coastal marine waters. To assess this impact, physicochemical parameters such as pH, salinity, total suspended solids (TSS), dissolved oxygen (DO), biochemical oxygen demand (BOD), and dissolved nutrients (NO2-N, NO3-N, NH4-N, PO4-P, SiO4-Si, total-N, and total-P) were analyzed from samples collected along 11 transects. Multivariate statistics and principal component analysis (PCA) were applied to the datasets, revealing four key factors that account for over 70.09% of the total variance in water quality parameters, specifically 25.01% for PC1, 21.94% for PC2, 13.13% for PC3, and 9.99% for PC4. The results indicate that the increase in nutrient and suspended solid concentrations in coastal waters primarily arises from weathering and riverine transport from natural sources, with nitrate sources linked to the decomposition of organic materials. Coastal Odisha was found to be rich in phosphorus-based nutrients, particularly from industrial effluents in Paradip and the Mahanadi, while ammonia levels were attributed to municipal waste in Puri. In contrast, the West Bengal coast exhibited higher levels of nitrogenous nutrients alongside elevated pH and DO values. These findings provide a comprehensive understanding of the seasonal dynamics and anthropogenic influences on coastal water quality in Odisha and West Bengal, highlighting the need for targeted conservation and management efforts.