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A compilation of data from several cruises between 1998 and 2013 was used to derive polynomial fits that estimate total alkalinity (AT) and total dissolved inorganic carbon (CT) from measurements of salinity and temperature in the Mediterranean Sea surface waters. The optimal equations were chosen based on the 10-fold cross-validation results and revealed that second- and third-order polynomials fit the AT and CT data respectively. The AT surface fit yielded a root mean square error (RMSE) of ± 10.6 μmol kg−1, and salinity and temperature contribute to 96 % of the variability. Furthermore, we present the first annual mean CT parameterization for the Mediterranean Sea surface waters with a RMSE of ± 14.3 μmol kg−1. Excluding the marginal seas of the Adriatic and the Aegean, these equations can be used to estimate AT and CT in case of the lack of measurements. The identified empirical equations were applied on the 0.25° climatologies of temperature and salinity, available from the World Ocean Atlas 2013. The 7-year averages (2005–2012) showed that AT and CT have similar patterns with an increasing eastward gradient. The variability is influenced by the inflow of cold Atlantic waters through the Strait of Gibraltar and by the oligotrophic and thermohaline gradient that characterize the Mediterranean Sea. The summer–winter seasonality was also mapped and showed different patterns for AT and CT. During the winter, the AT and CT concentrations were higher in the western than in the eastern basin. The opposite was observed in the summer where the eastern basin was marked by higher AT and CT concentrations than in winter. The strong evaporation that takes place in this season along with the ultra-oligotrophy of the eastern basin determines the increase of both AT and CT concentrations.