Seasonal hydrothermal variations on the land surface affect temperature as well suction profile in soil at shallow zones. For a Shallow Borehole Heat Exchanger (SBHE) buried not deep enough in the unsaturated soil, neglecting seasonal metrological conditions on the land surface may lead to design errors that may result in losing public's confidence. In this paper, an appropriate hydrothermal numerical analysis is used to predict seasonal hydrothermal fluctuations and SBHE performance of a site with a multi-layered soil system. The capacity of the numerical model is initially validated by the measured data from the thermal and humidity probes instrumented in a field located at Illkirch in the Alsace region (France). The results illustrate that the soil hydraulic conditions, as well as the soil thermal properties depend highly on the unsaturated soil properties in different layers. Then, the model is used to explore the performance of a SBHE installed in the same place over a year considering two different scenarios: constant inlet temperature and seasonal heat load. It has been found that the heat pump Coefficient of Performance (COP) in constant inlet temperature scenario remains almost stable during the service period. While in the case of seasonal heat load scenario, heat pump COP depends strongly on heat load and shows more variance. Eventually, the performance of the SBHE is estimated for the 5-year period considering the constant inlet temperature scenario. It has been found that the yearly Total Extracted Energy (TEE) decreases annually, while this reduction becomes less significant after the fourth year. The phenomenon illustrates that the SBHE is capable of outputting stable energy after reaching the equilibrium stage. (C) 2018 Elsevier Ltd. All rights reserved.