Estuaries are hotspots of intense biogeochemical cycling that regulate land–ocean exchanges and support a broad range of ecosystem services. They are a particularly important, still under-resolved, component of the global carbon cycle and often flash points for local socioeconomic conflicts. The mesotidal Guadalquivir estuary is fed by one of the Iberian Peninsula’s largest rivers, has a long history of anthropogenic manipulation, and hosts a surrounding population of over 1.7 million people. Monthly sampling of water biogeochemical properties (pigments, nutrients, alkalinity, pH, dissolved oxygen, and organic matter) was carried out in the estuary at 12 stations along its length between November 2007 and August 2009. pCO2 and dissolved inorganic carbon were calculated from total alkalinity and pH, allowing air–water fluxes (FCO2) and land–ocean transport to be estimated. The spatial distribution of oxygen concentration and suspended materials led to divide the system in three zones, the inner estuary (IE), the middle estuary (ME), and the lower estuary (LE), with a minimum oxygen zone and a maximum turbidity zone being found in the IE and ME, respectively. CO2 exchange pattern defined the estuary as a strong source being the IE the major contributor. Thus, estuarine waters were CO2 oversaturated with respect to the atmosphere during most of the study period, with average annual FCO2 values being 66.9 ± 18.6, 29.4 ± 20.3, and 3.4 ± 8.1 mmol C m−2 day−1 in the IE, ME, and LE, respectively. The average annual CO2 flux to the atmosphere was 36.4 ± 11.7 mol C m−2 year−1. The present study reinforces the heterotrophic status of the estuary in relation to the carbon system variable description.