Based on an unprecedented dissolved barium (D_Ba) data set collected in the Mediterranean Sea during a zonal transect between the Lebanon coast and Gibraltar (M84/3 cruise, April 2011), we decompose the D_Ba distribution to isolate the contribution of biogeochemical processes from the impact of the oceanic circulation. We have built a simple parametric water mass analysis (Parametric Optimum Multiparameter analysis) to reconstruct the contribution of the different Mediterranean water masses to the thermohaline structure. These water mass fractions have then been used to successfully reconstruct the background vertical gradient of D_Ba reflecting the balance between the large‐scale oceanic circulation and the biological activity over long time scales. Superimposed on the background field, several D_Ba anomalies have been identified. Positive anomalies are associated with topographic obstacles and may be explained by the dissolution of particulate biogenic barium (P_Ba barite) of material resuspended by the local currents. The derived dissolution rates range from 0.06 to 0.21 μmol m⁻² d⁻¹. Negative anomalies are present in the mesopelagic region of the western and eastern basins (except in the easternmost Levantine basin) as well as in the abyssal western basin. This represents the first quantification of the nonconservative component of the D_Ba signal. These mesopelagic anomalies could reflect the subtraction of D_Ba during P_Ba barite formation occurring during organic carbon remineralization. The deep anomalies may potentially reflect the transport of material toward the deep sea during winter deep convection and the subsequent remineralization. The D_Ba subtraction fluxes range from −0.07 to −1.28 μmol m⁻² d⁻¹. D_Ba‐derived fluxes of P_Ba barite (up to 0.21 μmol m⁻² d⁻¹) and organic carbon (13 to 29 mmol C m⁻² d⁻¹) are in good agreement with other independent measurements suggesting that D_Ba can help constrain remineralization horizons. This study highlights the importance of quantifying the impact of the large‐scale oceanic circulation in order to better understand the biogeochemical cycling of elements and to build reliable geochemical proxies.