This study presents the distribution and fluxes of dissolved nutrients in the Strait of Gibraltar, as well as their relationship to the microphytoplankton biomass distribution in the zone. In June and September 1997, the upper Atlantic inflowing waters west of the sill showed low nutrient concentrations. A significant increase was observed at the east of the sill. This increase can be attributed to mixing events at the sill between nutrient-rich Mediterranean Outflowing Waters (MOW) and the impoverished upper Atlantic Inflowing Waters (AW). Physical phenomena induced by tides at the sill act like an intermittent upwelling system and a part of the MOW nutrients re-circulate to the euphotic zone. Another factor is the injection of nutrient-rich North Atlantic Central Water (NACW) into the upper layer induced by the tides at the sill. These features along with the shallower position of the Atlantic-Mediterranean Interface (AMI) towards the north-east contribute to support high microphytoplankton biomass on the eastern side of the Strait. In the north-east, the injected nutrients are consumed by a high microphytoplankton standing stock. An accumulation of biomass is possible because the Atlantic-Mediterranean Interface (AMI) is shallower and the advection of cells is lower. In the south-east, AMI is deeper and the advection is higher. Nutrients are exported into the Albora´n Sea with low consumption by phytoplankton. Nitrate, phosphate and silicate fluxes between the Mediterranean Sea and Atlantic Ocean showed that Atlantic nitrate, phosphate and silicate concentrations compensate for about 21, 39 and 17% respectively of the outflowing losses. The results, extrapolated on an annual basis, show a net loss budget of nitrate, phosphate and silicate from the Mediterranean Sea of 3·00, 0·24 and 4·82106 tons year1, respectively. The evaluation of the flux of nutrients in the upper Atlantic current shows high variability due to biological and vertical mixing processes.