Aquifer thermal energy storage (ATES) is attained by storing thermal energy in aquifers, using the groundwater as a carrier for the heat. Hence, in ATES systems, the background groundwater flow velocity may affect the efficiency if a significant amount of stored heat is moved away from the storage well by advection. This paper presents an alternative solution to the typical “pump and dump” open-loop shallow geothermal system configuration using the ATES concept with a reversed extraction-injection well scheme. This particular placement is able to increase the energy efficiency of a conventional open-loop system while reducing the thermal impact downstream the system. The uni-directional ATES pumping scheme compensates the heat transport by groundwater flow extracting the groundwater from the downstream well and re-injecting back in the upstream well. This research presents a numerical feasibility study and sensitivity analysis of the effects of the well spacing, pumping scheme and groundwater flow velocity on the efficiency of a uni-directional ATES. Optimal combinations are suggested to ensure the maximum re-capture by the downstream well of the heat injected in the upstream well in the previous season and subject to thermal transport by advection, with a maximum heat recovery between 55 and 75 % depending on the conditions. The results of the modelling analysis showed that the optimal inter-well distance depends on the groundwater flow velocity and the total annual storage volume. This paper also demonstrates the mitigation effect of the thermal perturbation downstream of a uni-directional ATES compared to a conventional open-loop scheme.