The progressive electrification of the building conditioning sector in recent years has greatly contributed to reducing greenhouse gas emissions by using renewable energy sources, particularly shallow geothermal energy. This energy can be exploited through open and closed shallow geothermal systems (SGS), and their performances greatly depend on the ground/groundwater temperature, which can be affected by both natural and anthropogenic phenomena. The present study proposes an approach to characterize aquifers affected by high SGS exploitation (not simulated in this work). Characterization of the potential hydro/thermogeological natural state is necessary to understand the regional flow and heat transport, and to identify local thermal anomalies. Passive microseismic and groundwater monitoring were used to assess the shape and thermal status of the aquifer; numerical modeling in both steady-state and transient conditions allowed understanding of the flow and heat transport patterns. Two significant thermal anomalies were detected in a fluvio-glacial aquifer in southern Switzerland, one created by river water exfiltration and one of anthropogenic nature. A favorable time lag of 110 days between river and groundwater temperature and an urban hot plume produced by underground structures were observed. These thermal anomalies greatly affect the local thermal status of the aquifer and consequently the design and efficiency of current and future SGS. Results show that the correct characterization of the natural thermo-hydrogeological status of an aquifer is a fundamental basis for determining the impact of boundary conditions and to provide initial conditions required to perform reliable local thermal sustainability assessments, especially where high SGS exploitation occurs.