Measurements of the stable isotopic composition (δD(H2) or δD) of atmospheric molecular hydrogen (H2) are a useful addition to mixing ratio (χ(H2)) measurements for understanding the atmospheric H2 cycle. δD datasets published so far consist mostly of observations at background locations. We complement these with observations from the Cabauw tall tower at the CESAR site, situated in a densely populated region of the Netherlands. Our measurements show a large anthropogenic influence on the local H2 cycle, with frequently occurring pollution events that are characterized by χ(H2) values that reach up to ≈1 ppm and low δD values. An isotopic source signature analysis yields an apparent source signature below −400‰, which is much more D-depleted than the fossil fuel combustion source signature commonly used in H2 budget studies. Two diurnal cycles that were sampled at a suburban site near London also show a more D-depleted source signature (≈−340‰), though not as extremely depleted as at Cabauw. The source signature of the Northwest European vehicle fleet may have shifted to somewhat lower values due to changes in vehicle technology and driving conditions. Even so, the surprisingly depleted apparent source signature at Cabauw requires additional explanation; microbial H2 production seems the most likely cause. The Cabauw tower site also allowed us to sample vertical profiles. We found no decrease in χ(H2) at lower sampling levels (20 and 60 m) with respect to higher sampling levels (120 and 200 m). There was a significant shift to lower median δD values at the lower levels. This confirms the limited role of soil uptake around Cabauw, and again points to microbial H2 production during an extended growing season, as well as to possible differences in average fossil fuel combustion source signature between the different footprint areas of the sampling levels. So, although knowledge of the background cycle of H2 has improved over the last decade, surprising features come to light when a non-background location is studied, revealing remaining gaps in our understanding. Display omitted •Multi-year time series of H2 and δD(H2) were measured at a regional tall tower site.•The dataset contains the first measured δD height profiles in the boundary layer.•The features of the time series are consistent with large anthropogenic influences.•The apparent δD source signature is much lower than fossil fuel combustion estimates.•Both source signature and profiles suggest microbial H2 production around the tower.