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The development and application of a three-dimensional hydrodynamic and sediment transport model for the Gulf of Thermaikos, in the Northwestern Aegean Sea is presented. The processes that control the transfer of river-borne waters and fine-grained sediments are examined. These processes are: the overall basin circulation, the wind-driven flow, the buoyancy-driven flow that is associated with river plume dynamics and the sedimentation processes (flocculation, settling, deposition and erosion). We perform individual experiments, where only some of the processes are included, in order to study the different components of the transport mechanism separately. We also perform comprehensive experiments, where all processes are taken into account. It is found that a large percentage of the suspended particulate matter is deposited on the seabed of the Thermaikos Gulf and mainly near the river discharge sites. Although the sedimentation processes are of primary importance, the transport rates and pathways are greatly affected by the hydrodynamic processes that control circulation. Furthermore, the basin topography has a considerable impact on the transport, as the main rivers discharge near the narrow basin head and near areas of strong coastline curvature that act as sediment trapping zones. [Copyright &y& Elsevier]