Pollen is indispensable for life. But, as it may trigger allergic reactions, it can become a biological pollutant, thus requiring monitoring. In urban ecosystems, this is usually done with sampling at rooftop level; exposure to allergenic pollen at ground level is largely unknown. Using the Hirst-type methodology, we explore here how the qualitative, quantitative and phenological features of airborne pollen change horizontally, in different sites of the urban environment, and vertically, when pollen sources are primarily local. We sampled for two years in Thessaloniki, Greece, at six near-ground stations (at 1.5 m) and one at rooftop-level (30 m high). There was a large variability in quantitative pollen features among stations, but Urticaceae, Cupressaceae, Platanus, Pinaceae, and Quercus were the five most abundantly represented taxa in the air, both near the ground and at rooftop level, exceeding there an annual pollen integral of 1000 grains m−3. We found height to have a clear effect on pollen concentration: near the ground, it was three times higher for the entire pollen spectrum and up to 11 times higher for individual taxa. Assuming an exponential decay of pollen with distance from the ground, we calculated pollen concentration for the entire spectrum to decline to half the near-ground value every 19 m and at higher rates for individual taxa. Pollen season also varied largely among stations; a semi-natural station, next to a peri-urban forest, differed from the purely urban stations in having higher pollen concentration and shorter pollen season. For only two taxa, Urticaceae and Cupressaceae, pollen concentrations exceeded thresholds associated with high risk for more than 5% of the year. We conclude that pollen is far from homogeneously distributed within the urban environment, and that height has a strong effect on the low-altitude vertical profile of pollen. At an applied level, this study provides necessary information for more efficient monitoring of airborne pollen and for designing and managing urban green spaces, particularly under the current climate change and the associated higher demand for urban green.