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Estuarine carbonate chemistry predicts that thermodynamic equilibration during the mixing of freshwater with seawater will generate a carbon dioxide (CO2) sink in the case of warm and poorly buffered tropical rivers. The S ̃ao Francisco River estuary has historically become oligotrophic after the construction of a series of hydroelectric dams in its watershed, where organic matter and nutrients are retained. During two cruises in late winter (Aug. 2014) and early summer (Nov. 2015), dissolved inorganic carbon (DIC) and total alkalinity (TA) were found to increase linearly with salinity in the main estuarine channel, where water mixing required half a day, and showed nearly conservative behaviour. In the main channel, the water partial pressure of CO2 (pCO2) recorded at a 1-min frequency followed an asymmetric bell-shaped trend versus salinity, similar to the curve predicted by the thermodynamic conservative mixing of freshwater DIC and TA with seawater DIC and TA. The low (0–3) salinity region was always a source of atmospheric CO2, where despite low chlorophyll concentrations, a pCO2 diurnal change of approxi-mately 60 ppmv suggested the occurrence of photosynthesis in summer. At salinities above 3, undersaturated pCO2 values (down to 225 ppmv in winter and neap tides) and invasion of atmospheric CO2 of 0.38–1.70 mmol mL.