Thermal performance of the ground source heat pump (GSHP) system can be significantly affected by the complex geological substructures (such as ground stratification and groundwater advection). This study installed a seepage box inside the two-layered laboratory device to investigate the heat transfer processes of the unsaturated, saturated and infiltrated ground. Various operational and geological conditions were designed to study the temperature distributions at various locations and time experimentally and numerically. The groundwater effect on ground heat exchanger (GHE) thermal performance depends on the thermal properties, flow advection and the relationship between temperatures of the groundwater and ground. If the ground was partially saturated during the heat injection period, the cooling seepage will efficiently remove the heat of GHEs in upper-stream rather than those located in the bottom-stream. Meanwhile, the heat transfer can be enhanced if two legs of the U-tube vertical to the direction of groundwater seepage. The groundwater flow can redistribute the heat within the ground and showed a better recovery performance which advance an even temperature distribution by 3 h. The temperature and carried heat load of the cooler groundwater will increase during the heat injection experiment, and further contributed to various temperature distributions of ground at different locations and time. (C) 2019 Elsevier Ltd. All rights reserved.