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A physical-biological coupled model was used to estimate the effect of the physical processes at the Strait of Gibraltar over the biogeochemical features of the Atlantic Inflow (AI) towards the Mediterranean Sea. This work was focused on the seasonal variation of the biogeochemical patterns in the AI and the role of the Strait; including primary production and phytoplankton features. As the physical model is 1D (horizontal) and two-layer, different integration methods for the primary production in the Biogeochemical Fluxes Model (BFM) have been evaluated. An approach based on the integration of a production-irradiance function was the chosen method. Using this Plankton Functional Type model (BFM), a simplified phytoplankton seasonal cycle in the AI was simulated. Main results included a principal bloom in spring dominated by nanoflagellates, whereas minimum biomass (mostly picophytoplankton) was simulated during summer. Physical processes occurring in the Strait could trigger primary production and raise phytoplankton biomass (during spring and autumn), mainly due to two combined effects. First, in the Strait a strong interfacial mixing (causing nutrient supply to the upper layer) is produced, and, second, a shoaling of the surface Atlantic layer occurs eastward. Our results show that these phenomena caused an integrated production of 105 g C m− 2 year− 1 in the eastern side of the Strait, and would also modify the proportion of the different phytoplankton groups. Nanoflagellates were favored during spring/autumn while picophytoplankton is more abundant in summer. Finally, AI could represent a relevant source of nutrients and biomass to Alboran Sea, fertilizing the upper layer of this area with 4.95 megatons nitrate year− 1 (79.83 gigamol year− 1) and 0.44 megatons C year− 1. A main advantage of this coupled model is the capability of solving relevant high-resolution processes as the tidal forcing without expensive computing requirements, allowing to assess the effe