The recharge of karst aquifers is significant for the effective management of groundwater resources, and its estimation should be tailored to accommodate their specific hydrogeological characteristics. This study provides a two-step methodological approach for the determination of karst aquifer recharge. Initially, mean annual recharge rates were estimated in the karst system of Ziria (Southern Greece) utilizing the APLIS and modified APLIS methods in order to decipher which was the most suitable version for recharge assessments. The results indicated similar mean recharge rate values at 42.7% and 41.4%, respectively, but significant differences in the spatial distribution. The modified methodology emerged as a more accurate and realistic approach, mainly due to the incorporation of permeability assessments. The final phase of the methodological approach involved the application of modified APLIS in two additional karst hydrosystems, Planitero and Xiromero, while a quantitative cross-comparison of the recharge rates was obtained for a deeper understanding of the factors controlling the groundwater recharge process. In Ziria, recharge rates exhibit a relatively uniform distribution throughout the area, with a median value of 46.7%. Conversely, in Planitero, High recharge rates (60–80%) occupy 56.8% of the surface, while in Xiromero, Moderate recharge rates (40–60%) dominate, representing 53.4% of the land coverage. These variations underscore the spatial heterogeneity of recharge within the karst systems, highlighting the importance of considering local geological and hydrological conditions in its assessments. The methodological approach of this study is flexible and can be adapted to different karst sites for the determination of recharge regimes, contributing to the alleviation of the groundwater depletion issue.