Recent studies have provided a better understanding of carbonate system parameters and their spatial and temporal variability in several areas of the Mediterranean Sea. This study uses a new dataset that covered the entire Algerian Basin during the summer of 2014 (SOMBA cruise) to describe the distribution of carbonate system parameters. The findings show that almost the entire basin was a source of CO2 to the atmosphere during the studied period. Besides the well-known TrOCA (Tracer combining Oxygen, Carbon and total Alkalinity) approach, the study proposes new parametrization for the standard back calculation method to assess the anthropogenic carbon concentration. The results of both approaches yield similar distributions and concentration ranges (81 ± 4.3 and 69 ± 5.2 μmol/kg, respectively). This study assesses the errors for both approaches and emphasizes the importance of mesoscale and submesoscale structures on anthropogenic carbon sequestration and the distribution of carbonate parameters in the Algerian Basin. It shows that these features enhance basin ventilation and acidification. The first inventory of the anthropogenic carbon trapped by the Algerian Basin is estimated at 0.44–0.53 ± 0.06 Pg C, based on the new dataset.