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Hydrographic characteristics of the southwest coast of India and its adjoining Cochin backwaters (CBW) were studied during the summer monsoon period. Anomalous formation of anoxia and denitrification were observed in the bottom layers of CBW, which have not been previously reported elsewhere in any tropical estuarine systems. The prevalent upwelling in the Arabian Sea (AS) brought cool, high saline, oxygen deficient and nutrient-rich waters towards the coastal zone and bottom layers of CBW during the high tide. High freshwater discharge in the surface layers brought high amount of nutrients and makes the CBW system highly productive. Intrusion of AS waters seems to be stronger towards the upstream end (∼15 km), than had been previously reported, as a consequence of the lowering of river discharges and deepening of channels in the estuary. Time series measurements in the lower reaches of CBW indicated a low mixing zone with increased stratification, 3 h after the high tide (highest high tide) and high variation in vertical mixing during the spring and neap phases. The upwelled waters (O2 ⩽ 40 μM) intruded into the estuary was found to lose more oxygen during the neap phase (suboxic O2 ⩽ 4 μM) than spring phase (hypoxic O2 ⩽ μ10μM). Increased stratification coupled with low ventilation and presence of high organic matter have resulted in an anoxic condition (O2 = 0), 2-6 km away from barmouth of the estuary and leads to the formation of hydrogen sulphide. The reduction of nitrate and formation of nitrite within the oxygen deficient waters indicated strong denitrification intensity in the estuary. The expansion of oxygen deficient zone, denitrification and formation of hydrogen sulphide may lead to a destruction of biodiversity and an increase of green house gas emissions from this region. [ABSTRACT FROM AUTHOR]