The Mediterranean is a marginal sea displaying a peculiar biogeochemistry (enhanced deep respiration, non Redfieldian nutrient ratios, etc.). Here we discuss the different processes that may contribute to the observed peculiarities, inferred from the analysis of the nutrient data generated mostly during the last decade. Both nitrate to orthophosphate (N:P) and orthosilicate to nitrate (Si:N) ratios display a decreasing east-west gradient (N:P > 25 and Si:N > 1.3 in the eastern Mediterranean, and N:P ~ 20 and Si:N ≤ 1.0 in the western Mediterranean). The analysis of the transports at the two main straits (Gibraltar and Sicily) shows that the eastern Mediterranean is likely the site where the biological pump is non Redfieldian, whereas the Si:N > 1.3 in the eastern nutrient deep pool unexpectedly highlights an important role of the diatoms in the vertical export of matter. A quantitative analysis of the nutrient inputs and distributions suggests that the newly formed dense waters and the turbulent mixing transport a significant load of preformed organic and inorganic nitrogen from the surface, with the Levantine Intermediate Water being by far the most important player because of higher fraction of surface water in its mixture. Nutrient ratios and fluxes also suggests that nitrogen fixation, probably carried out by symbionts hosted by diatoms is taking place. The latter are relatively less important in the western than in the eastern basin. Those features may change in the next future if climate change or anthropogenic forcing alter the elemental fluxes at the boundaries.