The 3D structure of the Mygdonian sedimentary basin (N. Greece) is investigated. The aim of this study is to propose a 3D model of this sedimentary structure that can later be used to model the seismic records currently being obtained by the permanent accelerograph network operating in the area. This model builds on previous efforts and incorporates new data. The geometry and dynamic properties of the soil layers were inverted using data from microtremor array measurements, seismic refraction profiles, boreholes, and geotechnical investigations. Phase-velocity dispersion curves of Rayleigh waves were determined at 27 sites in the basin using the spatial autocorrelation method (SPAC) introduced by Aki [1]. S-wave velocity profiles were inverted from these dispersion curves and the whole valley structure was interpolated using our new results and all previously available data. The proposed 3D model describes the geometry and shear-wave velocities of the Mygdonian and pre-Mygdonian sedimentary systems, and the top bedrock surface. Our results indicate that this 3D model correctly reflects the geometry and dynamic properties of the sedimentary layers. The case of Euroseistest, where the subsoil structure is the result of bringing together many disparate data, could be used as an example for similar alluvial basins throughout the world, where usually only scarce data is available.