The ongoing climatic change, together with atmospheric pollution, influences the timing, duration and intensity of pollen seasons of some allergenic plant taxa. To study these influences, we correlated the trends in the pollen season characteristics of both woody (Fraxinus, Quercus) and herbaceous (Ambrosia) taxa from two pollen monitoring stations in Slovakia with the trends in meteorological factors and air pollutants during the last two decades. In woody species, the increased temperature during the formation of flower buds in summer and autumn led to an earlier onset and intensification of next year’s pollen season, especially in Quercus. The increase of relative air humidity and precipitation during this time also had a positive influence on the intensity of the pollen season of trees. The pollen season of the invasive herbaceous species Ambrosia artemisiifolia was prolonged by increased temperature and humidity during the summer and autumn of the same year, which extended the blooming period and delayed the end of the pollen season. From the studied air pollutants, only three were found to correlate with the intensity of the pollen season of the studied taxa, CO − positively and SO2 and NO2 − negatively. It is important to study these long-term trends since they not only give us valuable insight into the response of plants to changing conditions but also enable the prognosis of the exacerbations of pollen-related allergenic diseases.