During the CANIGO Project pHT and total alkalinity (AT) and continuous underway fugacity of carbon dioxide (fCO2) measurements were carried out in the Strait of Gibraltar in September 97 and February 98. The pH values describe the most representative water masses in the area, including the Levantine Intermediate Water (7.86) and West Mediterranean Deep Water (7.89). The linear relationships between the alkalinity (at all depths) and TIC (below the euphotic zone) with salinity were determined (AT=2353 (±0.4)+92.28 (±0.31) (S−36.0), r2=0.998 and CT=2119 (±1.4)+79.52 (±0.76) (S–36.0), r2=0.991). A net alkalinity outflow of –1.90±0.04 mol yr−1 was estimated. The normalised alkalinity and total inorganic carbon were higher in the Mediterranean waters than in the Atlantic. The Mediterranean seawater in the 200–400 m range shows higher CT values East (2323 μmol kg−1) rather than the West (2301 μmol kg−1) of the Strait of Gibraltar, which is related to mixing processes through the interface layer. Measures of fCO2 indicate that, in September 97, surface waters in the Strait of Gibraltar were acting as a source of CO2 of 3±8 mmol m−2 day−1. The fCO2 variation in surface water has been explained considering the contribution of dynamic processes, thermodynamic processes, exchange between air and seawater and biological processes. The seasonal fCO2 data record for the Strait of Gibraltar indicates that this coastal environment acts as a net sink for atmospheric CO2. The annual average flux of atmospheric CO2 into surface seawater is estimated to be −2.5 mol m−2 yr−1.