Over the last decades, the quality and quantity of the Mediterranean freshwater resources have significantly deteriorated due to climate change, unsustainable utilization, user conflicts, and seawater intrusions. On the small and remote island of Vis, where similar issues prevail, the need for alternative water management solutions has yielded managed aquifer recharge (MAR) as a promising option for increasing the safety and resilience of the local and autonomous water supply. By performing a cost–benefit analysis (CBA) to evaluate the feasibility of the deployment of an infiltration pond method in the Korita well field, the results evidenced a positive financial performance and sustainability of the proposed MAR solution. In addition, the overall economic benefits of the project, quantified through the willingness-to-pay method, significantly exceeded its costs, as evidenced by the high benefit/cost ratio of 2.83. The most significant uncertainty related to the infiltration pond method is represented by the high sensitivity to changes in the applied hydrological assumptions (i.e., the evaporation coefficient and number of annual infiltration pond recharges). This study aims to contribute to the understanding of interrelated socio-economic factors of MAR projects in karst aquifers, and represents the first of its kind in Croatia.