Submesoscale processes such as coastal water intrusions, frontal structures, and enhanced mixing play a critical role in regulating biogeochemical gradients in estuarine–coastal systems, yet observational evidence from tropical estuaries remains limited. This study investigates how submesoscale coastal intrusions associated with seasonal upwelling influence oxygen and nutrient dynamics in the Cochin estuary along the eastern Arabian Sea. High-resolution observations captured sharp spatial gradients in salinity, temperature, dissolved oxygen, and nutrients during contrasting seasonal phases. During the pre-upwelling period, intrusions of warm, saline, and oxygenated coastal waters (dissolved oxygen ~180 μM) propagated up to ~30 km into the estuary, forming pronounced estuarine–coastal fronts and strong horizontal gradients. In contrast, during the southwest monsoon, submesoscale intrusions of cold, saline, oxygen-depleted upwelled waters (dissolved oxygen ~25 μM) penetrated nearly 20 km upstream, generating persistent hypoxic zones and intensified vertical and lateral mixing. Phosphate concentrations exhibited strong submesoscale variability during both phases. Elevated phosphate levels (up to 3.2 μM) were observed in the upper estuary during pre-upwelling, while significantly higher concentrations (up to 4.1 μM) coincided with hypoxic intrusions in the lower estuary during upwelling. Phosphorus speciation indicates enhanced desorption from sediments under low-oxygen conditions, suggesting tight coupling between submesoscale physical processes and internal nutrient loading. A two-decade analysis reveals a gradual increase in phosphate concentrations, indicating that recurrent submesoscale intrusions of nutrient-rich, hypoxic coastal waters may be amplifying eutrophication in the estuary. These results demonstrate that submesoscale dynamics are key drivers of biogeochemical variability in tropical estuaries and must be explicitly considered in assessments of coastal ecosystem response to climate-driven changes in upwelling and circulation.