Aquifer thermal energy storage (ATES) is a technology with worldwide potential to provide sustainable space heating and cooling using groundwater stored at different temperatures. In areas with high ambient groundwater flow velocity (>25 m/y) thermal energy losses by displacement of groundwater may be prevented by application of multiple doublets. In such configurations two or more warm and two or more cold wells are aligned in the direction of the ambient groundwater flow. By controlling the infiltration and extraction rates of the upstream and downstream wells, the advection by ambient groundwater flow can be compensated by storing thermal energy through the upstream well, while re-extracting it from the downstream well. This study uses analytical and numerical tools and a case study to analyze the relevant processes, and provides guidelines for well placement and an operation strategy for ATES wells in aquifers with considerable groundwater flow. The size of the thermal radius relative to ambient groundwater flow velocity is an important metric. With multiple wells to counteract groundwater flow, this ratio affects the pumping scheme of these wells. The optimal distance between them is around 0.4 times the distance traveled by the groundwater in one year. A larger distance negatively affects the efficiency during the first years of operation.