We relate here the distributions of two carbonate system key properties (total alkalinity, AT; and total dissolved inorganic carbon, CT) measured along a section in the Mediterranean Sea, going from Marseille (France) to the south of the Cyprus Island, during the 2008 BOUM cruise. The three main objectives of the present study are (1) to draw and comment on the distributions of AT and CT in the light of others properties like salinity, temperature, and dissolved oxygen, (2) to estimate the distribution of the anthropogenic CO2 (CANT) in the intermediate and the deep waters, and (3) to calculate the resulting variation of pH (acidification) since the beginning of the industrial era. Since the calculation of CANT is always an intense subject of debate, we apply two radically different approaches to estimate CANT: the very simple method TrOCA and the MIX approach, the latter being more precise but also more difficult to apply. A clear picture for the AT and the CT distributions is obtained: the mean concentration of AT is higher in the oriental basin while that of CT is higher in the occidental basin of the Mediterranean Sea, fully coherent with the previous published works. Despite of the two very different approaches we use here (TrOCA and MIX), the estimated distributions of CANT are very similar. These distributions show that the minimum of CANT encountered during the BOUM cruise is higher than 46.3 μmol kg−1 (TrOCA) or 48.8 μmol kg−1(MIX). All Mediterranean water masses (even the deepest) appear to be highly contaminated by CANT, as a result of the very intense advective processes that characterize the recent history of the Mediterranean circulation. As a consequence, unprecedented levels of acidification are reached with an estimated decrease of pH since the pre-industrial era of −0.148 to −0.061 pH unit, which places the Mediterranean Sea as one of the most acidified world marine ecosystem.