Αn advanced three dimensional (3D) version of air mass Concentration Weighted Trajectory (CWT) model was applied, coupled with Mixed Layer Depth (MLD) estimations across the trajectory pathways. Three years daily PM2.5 composition measurements from an urban background site in Athens (Greece) were incorporated in the 3D-CWT model, to identify the atmospheric circulation patterns affecting PM2.5 constituent levels during cold (October 16th to April 15th) and warm (April 16th to October 15th) periods. The recirculation of local air masses inside the Mixed Layer (ML) during the cold period, was associated with accumulation of all PM2.5 constituents emitted from combustion sources (EC, OC, SO42−, NO3−, NH4+ and K+), whilst regional contributions of the same species were mainly associated with Northern airflows above the ML through Balkan Peninsula. In the cold period, transport of sea spray (Cl−, Na+ and Mg2+) and dust (Ca2+), from the Mediterranean and the Sahara desert respectively, was detected mainly through the ML, whilst sea salt from the Black Sea and dust from Balkan Peninsula were also transferred with Northern airflows above the ML. Contrariwise, transport from the Balkans area especially above the ML enriched the levels of all constituents of anthropogenic origin during the warm period, whilst the pattern of Saharan dust advections was also vertically extended above the ML. Conclusively, the implemented 3D-CWT model revealed a more detailed description of PM2.5 transport pathways in Athens, in comparison with the classic CWT model, by including the effect of MLD across the air mass trajectories.