Variations of carbon dioxide and radon content of cave air are presented as key parameters to assess the outgassing and isolation processes of a subterranean atmosphere. An exhaustive monitoring in the Castañar cave determined the temporal evolution of CO2 and 222Rn levels over a 12-month period, in order to characterise the mechanisms of these microclimatic processes. Concentrations of both gases show both seasonal variations and short-term fluctuations depending on several climatic factors: the air temperature difference between cave and exterior, cave air pressure, rainfall and anthropic factors including visits and duration of door opening. Over the course of an annual cycle, a cause-effect analysis has been conducted by stationary clustering of time series in terms of entropy of curves. Two opposing patterns of cave microclimate have been distinguished: (1) storage of trace gases in the cave reservoir during the cold-wet season, and (2) CO2 emissions during warm-dry season. The partial water filling of the porous system and fissures of the membranes covering the cave (host rock and soil) is determined by the external relative humidity (controlled by the external air temperature) as well as by rainfalls, which play a key role in confining the cave atmosphere.