The aim of this work was to understand the dynamics of CO2 in the atmosphere-soil-epikarst continuum of the Lascaux Cave site and to evaluate its impact on the hydrogeochemical signal of epikarstic waters. For these purposes, PCO2, δ13CCO2 and associated hydroclimatic parameters were recorded at different depths in soil and epikarst. In parallel, hydrogeochemistry of an epikarstic emergence (SAS1 spring) located in the entrance of the cave (6 m depth) was studied. PCO2 recorded in the soils underlines the seasonality and different levels of biogenic production according to the pedological facies and the physicochemical properties (higher in the calcisol than in the brunisol). CO2 efflux measurements show a seasonal evolution with maximum value (25 g m−2 d−1) in summer and minimum in winter (6 g m−2 d−1). It decreases during rain events because of the soil moisture increases which limits CO2 diffusivity. In the same way, seasonal processes of CO2 accumulation (winter and spring) and CO2 emission to the atmosphere (summer and autumn) are observed under the effect of soil moisture seasonal variations. These processes explain the very variable CO2 concentrations (0.6–6%) and δ13CCO2 values (−22.1 to −24.5‰) in the superficial epikarst (0–3 m depth). This CO2 accumulation explains the presence of higher CO2 contents in the epikarst than in the main production area: the soil. At deeper level exists a differentiated CO2 stock slightly variable (4–6%) with stable δ13CCO2 values from −22.7 to −21.7‰. Inter-annual variability of CO2 contents is influenced by the synchronicity or not of intense production and high soil moisture. A conceptual scheme of CO2 cycle is produced as a conclusion. The comparison with the evolution of water chemistry at the epikarstic emergence brings elements for understanding the acquisition of the karstification potential. Indeed, the seasonal evolution of the calcic carbonated mineralization of water is very well explained by the evolution of the CO2 contents in the epikarst (PCO2 at saturation with respect to calcite similar to the PCO2 of the air of the epikarst). In addition, the presence of two different CO2 compartments in the epikarst makes it possible to explain the variability of the chemical marking of water at the outlet depending on the flow conditions (transmissible and capacitive zones).