The Guadalquivir Estuary (main source of continental waters to the Gulf of Cadiz) has a carbonate basin, which enables the transport of inorganic carbon to adjacent coastal areas. Therefore, in order to study the dynamic of the carbonate system and its buffer capacity, a total of 12 samplings were carried out from 2017 to 2022. Samplings included longitudinal transects and tidal cycles in different seasonal and tidal conditions. Total alkalinity (TA) and dissolved inorganic carbon (DIC) showed increased values upstream, while calcium (Ca2+) presented the highest values in most of the marine samples. The ranges values obtained for these three variables were of 2180–5140 μmol kg−1, 430–3950 μmol kg−1 and 1295–10,855 μmol kg−1 for TA, DIC and Ca2+, respectively. Two buffer factors (βDIC and βH) were also calculated to study the variability of the buffer capacity of the Guadalquivir Estuary. These indicate that the estuary is well buffered for salinities above 10, while the inner part is more vulnerable to acidification effects. Using a non-linear 1D hydrodynamic model, net inorganic carbon system transports were calculated, showing that the Guadalquivir Estuary is exporting TA, DIC and Ca2+ to the Gulf of Cadiz.