Thermophysical properties of subsurface materials and groundwater flow strongly affect the heat exchange rates of ground coupled heat exchanger systems (GCHE). One popular method to estimate the mentioned thermal parameters is the interpretation of in situ thermal response test (TRT), but this method due to some simplifying assumptions could result in the overestimation of the number of needed heat exchangers. To overcome this problem, we propose to use finite element method to calculate the heat exchange rate of GCHE systems. Discrete Fracture Elements (DFE) has been integrated into the finite element matrix system to overcome the computational difficulties caused by the extreme disproportional geometries. To validate this method calculated data were compared with the data of a TRT and a cooling test measured at an implemented GCHE system. The correlation of calculated vs. measured data illustrate that the finite element model is able to better calculate the heat exchange rate than the TRT test. Next, we examined how the groundwater flow velocity (GWV), and the thermal properties in the grout affect the heat exchange rates of the GCHE. We concluded, that under 0.001 m/d GWV the effects are negligible, but over this value the heat exchange rates would increase rapidly, due to the advection effect of the groundwater motion.