The Mediterranean Sea is considered a small-scale ocean with high environmental variability and steep physicochemical gradients within a relatively restricted region. Its circulation is characterized by zonal gradients of physicochemical variables, with salinity, temperature, stratification and alkalinity all increasing towards the east. The generally low-nutrient (from oligotrophic to ultraoligotrophic) waters offshore stand in contrast to many near-shore regions, often containing coral and seagrass ecosystems, which are affected by human-induced eutrophication. Thus acidification is an additional anthropogenic pressure on Mediterranean Sea ecosystems, already suffering from overfishing, increasing sea surface temperatures, and invasions of alien species.

The Mediterranean Sea is both too complex and too small to be adequately resolved in global-scale climate and ocean-only models, some of which now include ocean biogeochemistry. To properly project how key biogeochemical and ecosystem processes will change, it is fundamental to adequately represent the general circulation of the Mediterranean basin, i.e., both the fine- scale processes that control it (e.g. eddies and deep convection), and the highly variable atmospheric forcing. With their relatively short residence times, Mediterranean Sea deep waters are likely to lag changes in surface waters by a few decades at most. Changes in deep-water formation sites, such as characterized by the dramatic shift with the Eastern Mediterranean Transient, are likely to coincide with changes in the hot spots where much of anthropogenic CO2 is taken up from the atmosphere and transferred into the deep sea (where it is stored for longer periods). The efficiency of carbon uptake and export from the surface waters to the basin interior depends on the relatively rapid time scales for surface-to-deep water exchange and the Mediterranean general circulation. Thus the combined effect of Mediterranean seawater acidification (absorbing anthropogenic CO2 per unit area), with low tropospheric warming on Mediterranean biogeochemistry, ecosystems, and the ecosystem services they support, through direct impacts on its highly adapted calcareous and non-calcareous organisms, may be larger than in other European regions.