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Carbonate aquifers are known as a major source for drinking water in the Mediterranean regions and in other part of the world. Therefore, qualitative and quantitative estimation of the groundwater resource are crucial, especially in area with densely populated areas. Stable water isotopes of surface and ground waters can be used to study water mixing, define recharge area, or identify fast infiltration in karst areas. It relies on (1) the variability of the input signal over space and time at a catchment scale, related to the rainfall isotopic signature, and (2) the flow, storage and mixing within the karst system, related to the soil -epikarst -unsaturated zone -saturated zone hydrodynamic behaviour. Mean groundwater isotopic signature can then be different from the mean total rainfall signature, depending on the effective rainfall amount. The isotopic signature of the recharge was calculated using a water balance model for two sampling sites in southeastern France. Soil and epikarst are modelled as a first compartment where evapotranspiration occurs, defined by its water capacity. An isotopic mixing balance model uses the calculated monthly effective rainfall and the analysed monthly mean isotopic water values of collected rainfall. This subsurface water capacity has a strong influence on the isotopic signature of the recharge and contributes to deplete the isotopic value of regional groundwater at the scale of a 2-year period. Keywords stable water isotopes• natural tracers • effective rainfall • recharge • carbonate aquifers • karst