Aquifer Thermal Energy Storage (ATES) can be a cost-effective and renewable geothermal energy source, depending on site-specific and thermohydraulic conditions. To design an effective ATES system having the effect of groundwater movement, understanding of thermohydraulic processes is necessary. The heat transfer phenomena for an aquifer heat storage are simulated by using FEFLOW with the scenario of heat pump operation with pumping and waste water reinjection in a two layered confined aquifer model. Temperature distribution of the aquifer model is generated, and hydraulic heads and temperature variations are monitored at the both wells during 365 days. The average groundwater velocities are determined with two hydraulic gradient sets according to boundary conditions, and the effect of groundwater flow are shown at the generated thermal distributions of three different depth slices. The generated temperature contour lines at the hydraulic gradient of 0.001 are shaped circular, and the center is moved less than 5 m to the direction of groundwater flow in 365 days simulation period. However at the hydraulic gradient of 0.01, the contour center of the temperature are moved to the end of east boundary at each slice and the largest movement is at bottom slice. By the analysis of thermal interference data between two wells the efficiency of the heat pump system model is validated, and the variation of heads is monitored at injection, pumping and no operation mode.