A method for improving the recovery efficiency of storing fresh water into an aquifer, the storing includes injecting the fresh water and extracting the injected fresh water by a single water storage system that includes at least one well penetrating into the aquifer, the method includes: providing a plurality of screens, each screen being located alongside a wall of at least one well, and each screen respectively allowing a flow of fresh water between an associated storage zone in contact with the screen and the well on which the screen is located; controlling the flow of fresh water through each one of the plurality of screens according to parameters provided from a storage model of the aquifer, the storage model describing a behavior of each storage zone.