The temperature of a 10-point vertical profile at the rock–atmosphere interface has been monitored since 2000 September in an underground vault at Aburatsubo, Japan, where resistivity variations have been reported in association with earthquakes. The non-ventilated vault is characterized by an annual temperature variation of about 1.2 ◦C peak to peak, compatible with thermal diffusion in the surrounding tuff rock, and by a long-term temperature increase of about 0.1 ◦C per year, possibly due to a local or global climate change. Owing to a careful relative calibration of the 10 thermistors used in this experiment, these data establish that the ceiling temperature is higher than the floor temperature by 0.04 to 0.28 ◦C. Transient temperature variations are observed in association with human presence or with typhoons, with a characteristic spatial pattern revealing structural heterogeneity.Variations with periods ranging from 1 day to 1 week, with an amplitude two time larger and a phase advance on the floor with respect to the ceiling, are observed from November to May. Variations with periods larger than 1 week, with an amplitude two times smaller and a phase lag on the floor with respect to the ceiling, are observed from June to October. These cycles are linked to the sign of the seasonal heat flux. We propose an interpretation in which heat transfer in the cavity is dominated by diffusion of water vapour from June to October (heat flux downwards, summer regime) and by convective water transport from November to May (heat flux upwards, winter regime). The water flow inferred from this model can be used to predict the water saturation of the rock as a function of time. Because of a permanent radiative heat flux from top to bottom, the upward water flow in the winter regime is larger than the downward water flow in the summer regime, resulting in a slow depletion of water from the rock below the cavity. This unbalanced water flow could contribute to an observed steady secular increase of rock resistivity, and possibly also to the long-term temperature increase of 0.1 ◦C per year. It is important to understand these processes in the context of underground geophysical observatories, underground waste storage and contaminant transport, as well as for the preservation of cultural items such as cave paintings.