Seawater intrusion is a worldwide increasing challenge, which lowers the freshwater availability by salination of fresh groundwater resources in coastal areas. The abstraction-desalination-recharge (ADR) methodology can combat seawater intrusion, whereby desalination is hereby the key factor for the overall efficiency of aquifer remediation. Which desalination technique is suitable within ADR depends on several factors and was not discussed before. We use a multi-criteria decision analysis and cost analysis to compare nanofiltration, reverse osmosis, electrodialysis, and (membrane) capacitive deionization and show for three case scenarios which desalination technique is most suitable within ADR. Overall, electrodialysis, nanofiltration, and reverse osmosis have shown the best utility value for saline groundwater salinity of 1–10 g L−1, whereby electrodialysis is more suitable for lower salinities. The lowest desalination costs are calculated for nanofiltration and reverse osmosis with 0.3–0.6 € m−3 depending on specific energy costs. Even capacitive deionisation can be a suitable alternative for low, slightly saline groundwater (1 g L−1) if the technology readiness level and a lifetime of electrodes increase and material costs decrease. These new insights provide a data analysis, costs, and decision support for desalination which are needed for the holistic approach to counteract seawater intrusion.