The Great Barrier Reef (GBR) is the largest reef system in the world. During winter (dry season), a relative increase of CO2 fugacity, together with a depletion in total alkalinity, was evident in the GBR lagoon water. This suggests the release of CO2 due to CaCO3 production in the lagoon. But, in detail, significant contribution from organic matter oxidation was also identified. Despite the dissolved carbon losses as carbonate, total dissolved inorganic carbon (DIC) concentration normalized at constant salinity was relatively uniform throughout the study area. This indicates the presence of external carbon input to the lagoon. The most likely source is river discharge, which carries sizeable amounts of dissolved and particulate organic carbon as well as DIC. The marine CO2 system of the GBR lagoon highlights the nature of tropical carbonate shelves as a strong alkalinity sink and a net oxidation site of land-derived organic carbon. ¿ 2001 American Geophysical Union