The ability of a three-dimensional sigma coordinate free surface model to reproduce the interfacial layer between the Atlantic and Mediterranean waters in the Strait of Gibraltar is verified. The model uses a coastal-following curvilinear orthogonal grid that includes the Gulf of Cadiz and the Alboran Sea, with very high resolution in the strait (less than 500 m). It is forced by imposing the two major semidiurnal tidal components (M2 and S2) along the Atlantic and the Mediterranean open boundaries. The main experiment covers an entire spring-neap cycle (fortnight period). Results show that the model is able to reproduce a thick interfacial layer that carries a substantial fraction of the total transport. The interfacial thickness is strongly modulated by tidal forcing that enhances the vertical exchanges between layers. In order to take into account the thick interfacial layer, a three-layer approximation is used to study the hydraulics. Results show that the exchange regime is intermittently maximal due to cyclically controlled regions over Camarinal Sill and within Tarifa Narrows. The analysis has been repeated in a two-layer framework to evaluate the impact of the introduction of an interfacial layer on the calculation of hydraulics. In the two-layer approximation, there is not any controlled region extending on the whole cross section, so the exchange is always submaximal. Concluding, the two-layer approximation underestimates hydraulic controls in the strait respect to the three-layer approach.