The long-range transport of particulates can substantially contribute to local air pollution. The importance of airborne pollen has grown due to the recent climate change; the lengthening of the pollen season and rising mean airborne pollen concentrations have increased health risks. Our aim is to identify atmospheric circulation pathways influencing pollen levels in three European cities, namely Thessaloniki, Szeged, and Hamburg. Trajectories were computed using the HYSPLIT model. The 4 day, 6 hourly three-dimensional (3-D) backward trajectories arriving at these locations at 1200 UT are produced for each day over a 5 year period. A k-means clustering algorithm using the Mahalanobis metric was applied in order to develop trajectory types. The delimitation of the clusters performed by the 3-D function “convhull” is a novel approach. The results of the cluster analysis reveal that the main pathways for Thessaloniki contributing substantially to the high mean Urticaceae pollen levels cover western Europe and the Mediterranean. The key pathway patterns for Ambrosia for Szeged are associated with backward trajectories coming from northwestern Europe, northeastern Europe, and northern Europe. A major pollen source identified is a cluster over central Europe, namely the Carpathian basin with peak values in Hungary. The principal patterns for Poaceae for Hamburg include western Europe and the mid-Atlantic region. Locations of the source areas coincide with the main habitat regions of the species in question. Critical daily pollen number exceedances conditioned on the clusters were also evaluated using two statistical indices. An attempt was made to separate medium- and long-range airborne pollen transport.