Subsurface environments are non-negligible contributors to the net carbon balance because they act as natural sinks of CO2 and are responsible for the efflux to the Earth’s atmosphere during their ventilation states. In this way, the characterization of the CO2 dynamics in these underground environments is essential to determine the gas exchange between both atmospheres. A complete microclimatic analysis and trace gas (CO2 and 222Rn) monitoring of Rull cave (southeast Spain) were conducted to characterize the natural dynamics and anthropogenic influence on the cavity. The analysis was accomplished by implementing wavelet analysis and resemblance techniques. This study enhances wavelet analysis as an efficient tool to analyse microclimatic time series, as it allows for the detection of the main periodicities of signals located in the time domain and the prevailing relationships between them. The analysis indicates that the low-frequency components of the signals were close to the identified annual natural cycles. For a 1-year cycle, the ventilation of the cavity causes the CO2 concentration to decrease from 3569 to 932 ppm in nearly 1 month, highlighting the existence of an output efflux from the cavity. On the contrary, the high-frequency components are linked to human perturbations caused by visitors in the cavity.