Managed aquifer recharge (MAR) constitutes a potential and promising solution to deal with several water management issues: water shortage, water level depletion, groundwater pollution, and saline water intrusion. Among others, the proper siting and cost evaluation of such a solution constitutes sources of uncertainty for the implementation of MAR schemes. In this study, we proposed a methodology for the assessment of the levelised cost of recharged water through an infiltration basin, including investment and operating costs. The method was implemented in a GIS-tool in order to build maps of levelised costs at the aquifer scale. The sensitivity analysis allows for the identification of the main natural characteristics (water quality and availability, etc.), technical (system life duration, recharge volume objective, etc.), and economic parameters (energy price, discount rate, etc.) that dominate the final cost estimate. The method was applied to a specific case study on an alluvial aquifer in Southern France. This new information on the economic feasibility of MAR scheme should be incorporated with more classical GIS-MCDA (relying on soil characteristics, aquifer storage capacity, land use, etc.) in order to properly site the system. Further information on financial and economic feedback from MAR implementation and research on the fate of recharged water are needed for a better benefits evaluation of this solution.