The Mediterranean Sea shows a peculiar anomaly in its nutrient pattern compared to the global ocean, as there is decrease in nutrient concentration from west to east. This feature has been attributed to the antiestuarine circulation at the Strait of Gibraltar, where an eastward flow of Atlantic nutrient-poor surface waters is compensated by a westward countercurrent of Mediterranean nutrient-rich deep waters. This water exchange has been suggested as the ultimate cause for the oligotrophy of the Mediterranean basin, even though only a few studies have accurately examined the magnitude of the nutrient flux through the Strait of Gibraltar. In this work, data from the Gibraltar Fixed Time series (GIFT) between 2005 and 2008 were used to assess nutrient distributions. Applying a two-layer model of water mass exchange and using the Mediterranean outflow recorded in situ, the net export of nutrients from the Mediterranean to the Atlantic was calculated as 139 and 4.8 Gmol yr−1 of nitrate and phosphate, respectively. The results also demonstrated that the Atlantic inflow is not nutrient depleted and in particular contains significant levels of phosphate, which is the limiting factor for biological productivity in the eastern Mediterranean. The distribution of the quasi-conservative parameter N* in the western and eastern basins indicated that nitrate-deficient surface waters are transformed into phosphate-deficient bottom waters by internal cycling processes. Therefore, phosphate depletion in the Mediterranean does not have its origin in the entry of a phosphorus-impoverished Atlantic inflow through the Strait of Gibraltar.