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Most studies implicitly consider soil carbon dioxide (CO2) efflux as the instantaneous soil respiration and thereby neglect possible changes in the amount of CO2 stored in the soil pore‐space. We measured the CO2 concentration profile of a well‐aerated soil continuously to evaluate the dynamics of the stored CO2 and to analyse the influence of environmental factors. For 25% of the observation period, changes in the amount of stored CO2 accounted for more than 15% of the soil‐CO2 efflux. The following factors were identified to interfere with steady‐state CO2 storage: (i) the fluctuating groundwater table altered the volume of the vadose zone, causing viscous airflow in air‐filled soil pores, (ii) atmospheric turbulence caused pressure‐pumping at the soil–atmosphere interface and (iii) intense rain greatly reduced the diffusivity of the uppermost soil layer. The friction velocity above the canopy was strongly correlated with fluctuations in the differential pressure between soil air and atmosphere, but no static pressure gradient could be detected because of the permeable nature of the soil. Unexpected short‐term declines in the soil CO2 concentration were observed during intense rainfall events. These declines were explained by the intensified CO2 saturation deficit of the infiltrating rainwater caused by the carbonate chemistry of the soil solution.

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