© 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.Groundwater depletion is considered a global problem. Coastal aquifers in arid and semiarid areas of the Mediterranean basin constitute typical examples of depleted aquifers. Güzelyurt (Morphou) Aquifer, the most important water resource for northern Cyprus, faces the problems of groundwater depletion and degradation of water quality near the coast due to significant amounts of groundwater extraction to satisfy the high demand. Recently, a water supply project, which transfers 75 million m3 of water from Turkey to northern Cyprus has been completed in June 2016 as a long-term remedy for serious water shortage problems in the northern part of the island. This project presents a unique opportunity for mitigating the depletion of the aquifer through relieving the existing high stress and helping to restore water levels by recharging the aquifer artificially with the available excess water. The objectives of this study are to develop 3-D detailed conceptual and numerical models of the aquifer, and to assess the potential for managed aquifer recharge by simulating the hydraulic behavior of aquifer under predefined artificial recharge and stress scenarios. The developed numerical model, after calibration and validation, was run for simulations of three different managed aquifer recharge scenarios focusing on the feasibility of restoring water levels to its “natural state” within a reasonable time frame. In all scenarios, a reasonable recovery of the groundwater depression zone was observed in about 11–14 years. However, the simulations showed that the aquifer has returned to its “natural state” in 48–73 years.