Thermal properties are very important for the design of ground heat exchangers (GHE). The line source model is typically used to identify these parameters, based on the inlet and outlet water temperature of an in-situ thermal response test (TRT). Since the model is based on thermal conduction, convection of groundwater can affect identification results. In this paper, a three-dimensional numerical simulation model was established to simulate the dynamic heat exchange for GHEs. A series of TRTs were conducted to analyse the effect of groundwater seepage on identification of thermal properties of soils. The equivalent thermal conductivity (ETC) was found to be increased gradually, while the equivalent volume heat capacity (EVHC) and the change rates of both parameters decreased with increases in groundwater velocity. The seepage direction was vital for identification, especially when the velocity was fast. The ETC was larger and the EVHC was smaller when the seepage direction was perpendicular as opposed to parallel to the buried pipe plane. The height of the seepage layer significantly affected identification results, and the greater the seepage velocity was, the more significant the effect was. In addition, the higher height led to the larger ETC and the smaller EVHC. The location of the seepage layer had little influence on results, but the ETC was larger and the EVHC was smaller if the location was closer to the ground surface. (C) 2018 Elsevier Ltd. All rights reserved.