The majority of Aquifer Thermal Energy Storage (ATES) systems studies have been conducted in aquifer systems located in large sand aquifers. Esker formation present a more challenging geometrical complexity compared to typical sand aquifers. This study aims to conduct comprehensive and long term performance evaluation of doublet type ATES system in esker geological formation in Stockholm, Sweden. The total heating and cooling used from the ATES are 673 MWh and 743 MWh respectively during the first 3 annual storage cycles of operation. The licensed total amount of water extraction and injection is 50 liters per second with undisturbed groundwater temperature of 9.5 degrees C. Over the first three storage cycles, the average injection and extraction temperatures for the warm side are 13.3 degrees C and 12.1 degrees C, and for the cold side 7.6 degrees C and 10.5 degrees C. The average temperature differences across the main heat exchanger from the ATES side are 4.5 K during winter and 2.8 K during summer which is 4-5 degrees lower than the optimum value. The average thermal recovery efficiency over the first 3 storage cycles were 47 % and 60 % for warm and cold storages respectively. The data analysis indicated annual energy and hydraulic imbalances which results into undesirable thermal breakthrough between the warm and cold side of the aquifer. This was mainly due to suboptimal operation of the building energy system which led to insufficient heat recovery from the warm side, and subsequently insufficient cold injection in the cold wells, despite the building heating demand and the available suitable temperatures in the ATES. The cause of the suboptimal operation is the oversizing of the heat pumps which were designed to be coupled to larger thermal loads as compared to the ones in the final system implementation. As a result, the heat pumps could not be operated during small-medium loads. Additionally, the paper discusses the limitations of currently used energy and thermal key performance indicators (KPI) for ATES and propose an additional thermal KPI named heat exchanger efficiency balance (beta HEX) that connects and evaluate the optimum operational point of temperature differences from both the building and ATES prospective. In addition to ATES energy and hydraulic KPIs, beta HEX can contribute in providing more complete picture on the ATES-building interaction performance as well as highlights if the losses in energy recovery from ATES are due to the subsurface processes or building energy system operation which has been proven to be critical for the optimum ATES performance.