The number of borehole heat exchangers (BHEs) is continuously rising in Europe. Just like other energy producing technologies, there are risks associated with BHE systems. Therefore, guidelines are necessary for regulating the construction and operation of such installations. In order to be able to trade-off the expected benefits against possible risks, knowledge about the local hydrogeological conditions, and the processes taking place, is required. Using the geothermal energy use concept developed for Canton Basel-Landschaft as an example, it is shown how the approval of BHE systems can be regulated in a differentiated way, and how the geological characteristics of a region can be integrated into a geothermal energy use concept. In particular, karst areas, areas with the risk of ground swelling and subrosion, water protection areas, and areas with multiple or confined aquifers are considered. The article aims at making a contribution to the present societal discussion about the benefits and risks of shallow geothermal energy systems by describing the risks associated with BHEs, and by presenting options to account for these risks in approval practice.