Abstarct: Energy production and transformation processes are often associated with pollution in the environment. In order to make a solution for reduction of pollution, human has turned to energy saving and clean energy technologies. One of these techniques is groundwater heat pump (GWHP) system that uses from constant temperature of the ground in low depths as a source of clean and renewable energy for heating and cooling. In this technique groundwater with constant temperature is extracted by pumping wells, passed through the heat exchanger and then returned to aquifer through the injection wells. Owing to the mathematical similarities between heat and mass transport, the computer program MT3DMS that is an applied code in mass transport modeling was used for simulating heat transfer in groundwater in this study and groundwater flow and heat transport modeling was performed in a hypothetical aquifer. The results show that a thermal plume is developed around the injection well due to the energy exchanges in GWHP system. This plume is regarded as an indicator of the impact of the injected water temperature on the underground source. baxsed on the results of this study the extent and direction of the thermal plume are directly affected by the hydrogeological parameters such as hydraulic conductivity, hydraulic gradient and porosity of aquifer. As the only parameters which lixnk the heat pump system with groundwater are discharging flow rate and temperature, so their affecting factor are also influence performance of the GWHP system. The important effective factors on flow rate of the discharging well which were investigated in this study are included as water table fluctuation, clogging, impact of neighboring wells and laxyering and change in aquifer characteristics. The main factors affecting groundwater temperature as the input to GWHP system were also considered to be depth to water table, location of discharging and injecting wells and flow direction. Change in these parameters can affect the performance of the GWHP system, as well.