Measurements of the soil’s surface for natural hydrogen exploration may be considered dubious due to several artefacts. For instance, drill bit metamorphism and superficial biological activity can induce hydrogen generation that is irrelevant for energy exploration. Furthermore, adsorbed hydrogen can be released through drilling and pumping operations. Here, we present a model of the hydrogen signal in soil when air containing traces of hydrogen is pumped out. According to this model, observed hydrogen recharge after several minutes would indicate active hydrogen flow during the measurements, whereas its absence may indicate adsorbed hydrogen in the soil or artefacts. This model allows us to quantify the hydrogen flow responsible for concentration anomalies in soils. It is consistent with the hypothesis that hydrogen emission from soils is not constant but rather occurs in the form of gas flushes over a period of a few days.