This study presents a simple framework methodology for selecting the most appropriate locations for managed aquifer recharge (MAR). The proposed approach is applicable to aquifers that are located in coastal or mountainous areas and are used either for agricultural or industrial (e.g., mining) activities. A characteristic case study for the identification of the areas that are the most suitable for aquifer recharge using a GIS multi-criteria decision analysis (GIS-MCDA) method by means of MAR type spreading methods is the Geropotamos basin, Crete, Greece. Criteria combining a high relevance and high data availability, and providing unique information, were selected to assess the suitability of aquifer recharge in the basin. The criteria applied to evaluate the sites’ suitability for MAR spreading methods are hydrogeology, slope, land use, rainfall, groundwater level, soil texture and distance to source water. This study uses the ‘Pairwise comparison’ to assign criteria weights, as part of the Analytic Hierarchy Process (AHP), and examines four different scenarios. In all four scenarios, downstream areas, and close to the river Geropotamos, coincide as the most appropriate for aquifer recharge.