A methodology describing matter transfer in coastal basins connected with a small channel is presented. More specifically, the spreading of suspended particulate matter after the sudden release from a source in Thermaikos Bay (NW Aegean Sea) and the effect to the adjacent Toroneos bay through the Potidea Channel was examined via mathematical modelling. A 2DH hydrodynamic model was applied coupled to a quasi 3D transport model. A key point was the computation of the probability for a particle reaching the computational cell, adjacent to the channel, to pass the small channel of subgrid scale and reach the adjacent bay. For that reason, another, second couple of a small scale high resolution 2DH hydrodynamic and transport models, focusing on vicinity of the channel was applied so that the aforementioned probability could be calculated for the large scale model. The simulations referred to the wind generated circulation and resulted to the eventual distribution of the particle concentrations over the two bays, thus, informing us about the potential matter transfer through the Potidea channel. It was finally shown that only a minor amount of material crosses the channel and escapes Thermaikos to reach Toroneos, under the influence of SW, NW and W winds. [ABSTRACT FROM AUTHOR]