Pulicat lagoons play an essential role as habitats for a wide variety of species, which are important for human nutrition and economic endeavours, as well as for their substantial contributions to biogeochemical and hydrological processes. This study examines the environmental dynamics of Pulicat Lagoon, India, emphasizing its significance as a coastal ecosystem. Hydrodynamic studies reveal that tidal action is the primary driver of circulation in the lagoon, with water surface elevation fluctuating from − 0.3 m during neap tides to 0.67 m during spring tides. High water levels in summer reached + 0.63 m. Maximum current speeds were observed between Stations 1 and 3, decreasing toward the lagoon's mid-section, while the western part (near Sunnambukkulam) experienced currents of less than 0.1 m/s. Simulation results reveal that seawater parcels travel approximately 15.8 km into the lagoon during the southwest monsoon. The study further examines the ecological implications of these hydrodynamic conditions, revealing that salinity, dissolved oxygen, and water transparency are significantly influenced by chlorophyll-a concentrations. Nitrogen emerged as the limiting nutrient during the monsoon, while phosphate became limiting in the post-monsoon and summer periods. Notably, riverine imports of Dissolved Inorganic Phosphorus (DIP) surged from 41.3 × 103 mol P d⁻1 in the dry season to 177.2 × 103 mol P d⁻1 in the wet season. The lagoon's negative VRDINR values indicated a consistent output of Dissolved Inorganic Nitrogen (DIN), whereas positive VXDINX values suggested nitrogen import from the ocean during specific seasons. Moreover, modelling results showed that rapid tidal mixing constrained nutrient availability and reduced water transparency in certain areas. The present study concludes by advocating for sustainable management practices to enhance nutrient distribution and bolster the overall health of this critical ecosystem.