Total mercury concentrations were determined in water samples from ten vertical profiles in the western Mediterranean. Most Hg concentrations ranged from 0.5 to 4 pM, with a geometric mean of 2.26 pM. Such concentrations are in the same range as those measured in the North Atlantic and equatorial Pacific waters. There is no indication that the presence of geothermal activity or cinnabar deposits around the Mediterranean basin induces higher mercury concentrations in waters. Vertical concentration profiles were characterized by a maximum just below the thermocline, which is mainly developed in regions with relatively high primary production in the overlying waters. These observations support the remobilization model according to which, the mercury, associated with degradable organic matter, is solubilized from the particles accumulated in the thermocline layer. Additional measurements of certain mercury species, including reactive mercury (HgR) and gaseous species [elemental mercury (Hg°) and dimethylmercury (DMHg)], were performed on three profiles in the Alboran Sea and the Strait of Gibraltar. While 50% of the total mercury consisted of unidentified organic association, a maximum of the three determined species were observed below the thermocline: up to 0.71 pM, 0.43 pM and 0.30 pM for HgR, Hg° and DMHg, respectively. DMHg and Hg° appear to be formed in the low oxygen zone. A specific methylation rate of 3 × 10−9 s−1 can be estimated, which is six times higher than the values proposed for the North Atlantic waters (Mason et al., 1995a, Water, Air and Soil Pollution, 80, 665–677).The mass balance budget in the western Mediterranean shows that, while the total mercury exchanges at the straits are not unbalanced, mercury enters the Mediterranean as inorganic mercury and is exported to the Atlantic Ocean partially as methylated species. Riverine input is mainly composed by particulate mercury which is readily accumulated in coastal sediments. The dissolved mercury flux from non-marine sources is largely dominated by atmospheric deposition, which is one order of magnitude higher than riverine input. The mercury accumulation rate in the sediments is quantitatively equivalent to the atmospheric inputs, but mainly constituted by terrestrial material deposited nearshore. On the basis of ☐-core analyses and the global model of Mason et al. (1994a, Geochimica et Cosmochimica Acta, 58, 3191–3198) and present results the pre-industrial Hg riverine, atmospheric and sedimentation fluxes are estimated to have been about one-third the current one.