Abstract The Member States of the European Union pledged to reduce greenhouse gas emissions by 80–95% by 2050. Shallow geothermal systems might substantially contribute by providing heating and cooling in a sustainable way through seasonally storing heat and cold in the shallow ground (<200 m). When the minimum yield associated with the installation of a cost-effective aquifer thermal energy storage (ATES) system cannot be met, borehole thermal energy storage, relying mostly on the thermal conductivity of the ground, is proposed. However, for large-scale applications, this requires the installation of hundreds of boreholes, which entails a large cost and high disturbance of the underground. In such cases, ATES systems can nevertheless become interesting. This paper presents a case study performed on a Ghent University campus (Belgium), where the feasibility of ATES in an area with a low transmissivity was determined. The maximum yield of the aquifer was estimated at 5 m 3 /h through pumping tests. Although this low yield was attributed to the fine grain size of the aquifer, membrane filtering index tests and long-term injection tests revealed that the clogging risk was limited. A groundwater model was used to optimize the well placement. It was shown that a well arrangement in a checkerboard pattern was most effective to optimize the hydraulic efficiency while maintaining the thermal recovery efficiency of the ATES system. Hence, for large-scale projects, efficient thermal energy storage can also be achieved using a (more cost-effective) ATES system even in low-permeability sediments.