The effective ground thermal conductivity and borehole thermal resistance, which are key parameters in the design of borehole heat exchangers (BHEs), are often determined on the basis of an in situ thermal response test (TRT). Two experimental set-values--volumetric flow rate and heat injection rate--of the TRT apparatus are decided before performing the test. In general, the latter is often determined by rule of thumb, because of the lack of guidelines and systematic analysis regarding the setting of the TRT apparatus for various ground conditions. However, if the ground is saturated and has high porosity and there is no groundwater flow, the natural convection induced by density differences can be an important factor for the heat transfer in a porous medium. This paper focuses on heat transfer by natural convection around the BHE and its impact on the estimation of the thermal properties of the ground. By using the finite element method, we reproduced the TRT of a vertical closed loop BHE backfilled with coarse sand and gravel. We found that the natural convection around the BHE is an important factor that affects the estimation of thermal properties of soil and the operational performance of the ground source heat pump.