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Abstract. The research objective is the detection of the mechanism of the water mass exchange through a navigational channel connecting two adjacent coastal basins. The research involves the application of a mathematical model in parallel to in-situ measurements. The hydrodynamic circulation in the greater area of the NW Aegean Sea is modeled by means of a barotropic circulation model. Wind, Coriolis and Tide are the main forcings taken into account. The flow through the channel is resolved at a subgrid scale by means of a local open channel flow model. The comparison between field measurements, recorded during a limited period, and the model results supports the model verification. The study is integrated by an operational application of the model under various realistic forcings. The results help to gain a better understanding of the mechanisms regulating the water mass exchange and the consequent interaction between two adjacent connected coastal basins. From the case study of the Potidea channel it is revealed that the water mass exchange under mean wind forcing is of the same order as the one induced by the tidal forcing.