Abstract. In contrast to its small surface area, the coastal zone plays a disproportionate role in the global carbon cycle. Carbon production, transformation, emission and burial rates at the land–ocean interface are significant at the global scale but still poorly known, especially in tropical regions. Surface water pCO₂ and ancillary parameters were monitored during nine field campaigns between April 2013 and April 2014 in Guanabara Bay, a tropical eutrophic to hypertrophic semi-enclosed estuarine embayment surrounded by the city of Rio de Janeiro, southeast Brazil. Water pCO₂ varied between 22 and 3715 ppmv in the bay, showing spatial, diurnal and seasonal trends that mirrored those of dissolved oxygen (DO) and chlorophyll a (Chl a). Marked pCO₂ undersaturation was prevalent in the shallow, confined and thermally stratified waters of the upper bay, whereas pCO₂ oversaturation was restricted to sites close to the small river mouths and small sewage channels, which covered only 10 % of the bay's area. Substantial daily variations in pCO₂ (up to 395 ppmv between dawn and dusk) were also registered and could be integrated temporally and spatially for the establishment of net diurnal, seasonal and annual CO₂ fluxes. In contrast to other estuaries worldwide, Guanabara Bay behaved as a net sink of atmospheric CO₂, a property enhanced by the concomitant effects of strong radiation intensity, thermal stratification, and high availability of nutrients, which promotes phytoplankton development and net autotrophy. The calculated CO₂ fluxes for Guanabara Bay ranged between −9.6 and −18.3 mol C m⁻² yr⁻¹, of the same order of magnitude as the organic carbon burial and organic carbon inputs from the watershed. The positive and high net community production (52.1 mol C m⁻² yr⁻¹) confirms the high carbon production in the bay. This autotrophic metabolism is apparently enhanced by eutrophication. Our results show that global CO₂ budgetary assertions still lack information on tropical, marine-dominated estuarine systems, which are affected by thermal stratification and eutrophication and behave specifically with respect to atmospheric CO₂.