Results are presented of a comprehensive thermal impact study on an aquifer thermal energy storage (ATES) system in Bilthoven, the Netherlands. The study involved monitoring of the thermal impact and modeling of the three-dimensional temperature evolution of the storage aquifer and over- and underlying units. Special attention was paid to non-uniformity of the background temperature, which varies laterally and vertically in the aquifer. Two models were applied with different levels of detail regarding initial conditions and heterogeneity of hydraulic and thermal properties: a fine-scale heterogeneity model which construed the lateral and vertical temperature distribution more realistically, and a simplified model which represented the aquifer system with only a limited number of homogeneous layers. Fine-scale heterogeneity was shown to be important to accurately model the ATES-impacted vertical temperature distribution and the maximum and minimum temperatures in the storage aquifer, and the spatial extent of the thermal plumes. The fine-scale heterogeneity model resulted in larger thermally impacted areas and larger temperature anomalies than the simplified model. The models showed that scattered and scarce monitoring data of ATES-induced temperatures can be interpreted in a useful way by groundwater and heat transport modeling, resulting in a realistic assessment of the thermal impact.