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Quantifying groundwater recharge in carbonate aquifers located in semi-arid regions and subjected to intensive groundwater use is no easy task. One reason is that there are very few available methods suitable for application under such climatic conditions, and moreover, some of the methods that might be applied were originally designed with reference to non-carbonate aquifers. In addition, it is necessary to take into account the fact that, in any given aquifer, groundwater recharge is modified by the groundwater exploitation. Here we focus on four methods selected to assess their suitability for estimating groundwater recharge in carbonate aquifers affected by intensive exploitation. The methods were applied to the Estepa Range aquifers of Seville, southern Spain, which are subjected to different degrees of exploitation. Two conventional methods were used: chloride mass balance and daily soil-water balance. These results were compared with the results obtained by means of two non-conventional methods, designed for application to the carbonate aquifers of southern Spain: the APLIS and ERAS methods. The results of the different methods are analogous, comparable to those obtained in nearby non-exploited carbonate aquifers, confirming their suitability for use with carbonate aquifers in either natural or exploited regimes in a semi-arid climate.