Observations along 10 shelf transects in 2012 near 10°N in the southeastern Arabian Sea revealed the usual warm oligotrophic conditions during the winter monsoon and upwelling of oxygen‐deficient, nutrient‐rich cool water during the summer monsoon (SM). By changing an oligotrophic to a nutrient‐replete condition, the upwelling is the major process that regulates the biogeochemistry of this shelf. Its onset is perceptible at 100 m depth between January and March. The upwelling reaches the surface layer in May and intensifies during June–July but withdraws completely and abruptly by October. Despite the nutrient injection, the primary production during SM, integrated for euphotic zone, is comparable to that during the preceding spring intermonsoon (SIM). Again, as usual, the high oxygen demand coupled with low concentration in the upwelled subsurface waters causes severe oxygen depletion below the shallow pycnocline. The oxygen concentrations/saturations of 2012 on the midshelf are similar from those of mid‐1958 to early 1960, except for marginally higher values during the peak upwelling period due to relatively weak upwelling in 2012. This implies little anthropogenic influence on coastal hypoxia unlike many other coastal regions. In 2012, the inner shelf system shifted from net autotrophy in SIM to net heterotrophy in SM but on an annual basis it was net autotrophic (gross primary production to community respiration ratio, GPP/R:1.11 ± 0.84) as organic production exceeded consumption.

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 ecosystem along 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.

The growing number of oxygen-deficient coastal zones around the world and their impacts on marine life has always been a controversial issue as their development is largely attributed to anthropogenic activities which can be mitigated by human actions. However, contrary to this prevailing understanding, we show here for the first time, using new coherent datasets from estuaries to coastal to offshore regions, that the world’s largest hypoxic-anoxic zone along the west coast of India is formed through a natural process, i.e. upwelling of deoxygenated waters during the summer monsoon. We further demonstrate that the persistence and extent of this coastal oxygen deficiency depend on the degree of deoxygenation of source waters for the upwelling. Consequently, the anoxia is confined only to the central shelf between 11° and 18° N, which is equivalent to almost half of the western Indian shelf, where upwelling brings suboxic waters from the core oxygen minimum zone in the Arabian Sea.