Carbon biogeochemistry of a tropical ecosystem (The Cochin Estuary, India) undergoing increased human intervention was studied during February (premonsoon), April (early monsoon) and September (monsoon) 2005. The Cochin estuary sustains high levels of pCO2 (up to 6000 μatm) and CO 2 effluxes (up to 274 mmolC m-2 d-1) especially during monsoon. A first-order estimate of the carbon mass balance shows that net production of dissolved inorganic carbon is an order of magnitude higher than the net loss of dissolved and particulate organic carbon from the estuary. This imbalance is attributed to the organic inputs to the estuary through anthropogenic supplies. The bacteria-mediated mineralization of organic matter is mainly responsible for the build-up of pCO2 and increased CO 2 emission to the atmosphere indicating heterotrophy. The linear correlation between excess CO2 and apparent oxygen utilization indicates respiration as the chief mechanism for CO2 supersaturation. An increase in the net negative ecosystem production (-ve NEP) between premonsoon (-136 mmolC m-2 d-1 or -376 MgC d-1) and monsoon (-541 mmolC m-2 d-1 or -1500 MgC d -1) is supported by a corresponding increase in O2 influxes from 17 mmol O2 m-2 d-1 (126 MgC d-1) to -128 mmol O2 m-2 d-1 (-946 MgC d-1) and CO2 emissions from 65 mmolC m-2 d-1 (180 MgC d-1) to 267 mmolC m-2 d -1 (740 MgC d-1). There is a significant north-south gradient in metabolic rates and CO2 fluxes attributable to the varying flow patterns and anthropogenic inputs into the estuary. The study reveals that the Cochin estuary, a previously autotrophic (CO2 sink) system, has been transformed to a heterotrophic (CO2 source) system following rapid urbanization and industrialization. Moreover, the export fluxes from the Cochin estuary appear to be quite important in sustaining net heterotrophy in the southeastern Arabian Sea. © 2009 Springer Science+Business Media, LLC.