A rapidly growing amount of office buildings in the Netherlands is using an Aquifer Thermal Energy Storage (ATES) system. An essential condition for optimal ATES operation is the thermal balance of the system. Office buildings typically store much more heat than cold, causing the entire underground slowly to heat up and causing cooling capacity problems on the long term. A reference model is constructed based on the Kropman Utrecht case study building and contains three main blocks: The ATES, Heating/Ventilation/Air-conditioning (HVAC) and load simulation. For the ATES system a method is developed to reconstruct the injected water temperatures and volumes, because these are not measured in the case study installation. The HVAC and load simulation models are based on logged building management system (BMS) data. The use of BMS data has the large advantage that models are easily configured and can automatically adjust to changes in the building. Using MPC it was possible to keep the ATES in balance over a simulated 20 years period. For the case study building it can be concluded that MPC, using the developed reference model, is capable of automatically maintaining the ATES balance. Because the case study building type and size is comparable to the majority of the new Dutch office buildings, it is expected that large parts of the method are universally applicable.