Shallow Geothermal Energy (SGE) exchanges heat with the ground. In continuous, long-term operation, the initial temperature field can be disturbed, and subsurface thermal changes can be developed. In this paper, the thermal impact of a SGE system under a Mediterranean climate is handled. Temperature monitoring was conducted on 15 investigation boreholes equipped with a total of 92 thermal sensors placed at specific depths. Investigation boreholes were drilled 1–2 m from SGE system borehole heat exchangers installed in a university building. The analysis handles a one-year monitoring period of SGE system operation. Temperature depth profiles, reaching up to 140 m depth, were registered with a 10 min time step, resulting in a large amount of data. Ground thermal conductivity was estimated experimentally and semi-empirically, allowing us to obtain, using a numerical model, the initial undisturbed ground temperature profiles and compare them with the monitored values. Climate data were recorded by the university meteorological station. Globally, the measured and computed data were coherent, and a non-negligible impact of the SGE system operation in the first year was observed. The building orientation as well as the nearby departments had significant impacts on the shallow ground temperature. Maximum ground temperature changes observed at depths higher than 10–20 m, ranging from 2 to 3 °C as observed in different boreholes, indicate that the system is operating efficiently.