Quantification of nitrogen (N) transformation rates in tropical estuarine-coastal water coupled systems undergoing anthropogenic disturbances is scant. A thorough understanding of these metabolic rates is required to evolve a mitigation strategy to save such systems from further degradation. Here, we report the first measurements of ammonium (NH4 +) and nitrate (NO3 −) uptake along with N2 fixation rates in the Cochin estuary, a tropical eutrophic ecosystemalong the west coast of India, and two transects (off Cochin and off Mangalore) in the coastal Arabian Sea. In general, the Cochin estuary sustained higher uptake rates of NH4 + (0.32– 0.91 μmol N l−1 h−1) and NO3 − (0.01–0.38 μmol N l−1 h−1) compared to coastal waters. The N uptake in the nearshore waters of Cochin transect (NH4 +:0.34 μmol N l−1 h−1 and NO3 −:0.18 μmol N l−1 h−1) was influenced more by estuarine discharge than was the Mangalore transect (NH4 +:0.02 μmol N l−1 h−1 and NO3 −:0.03 μmol N l−1 h−1). Despite high dissolved inorganic nitrogen (DIN) concentrations, the Cochin estuary also showed higher N2 fixation rates (0.59– 1.31 nmol N l−1 h−1) than the coastal waters (0.33–0.55 nmol N l−1 h−1).NH4 + was the preferred substrate for phytoplankton growth, both in the Cochin estuary and coastal waters, indicating the significance of regenerative processes in primary production. A significant negative correlation between total nitrogen (TN): total phosphorus (TP), and NH4 + uptake (as well as N2 fixation) rates in the estuary suggests that nutrient stoichiometry plays a major role in modulating N transformation rates in the Cochin estuary