A mathematical model is developed for predicting the temperature distribution in an aquifer thermal energy storage (ATES) system, which consists of a confined aquifer bounded from above and below by the rocks of different geological properties. The main transfer processes of heat include the conduction and advection in the aquifer and the conduction in the rocks. The semi-analytical solution in dimensionless form for the model is developed by Laplace transforms and its corresponding time-domain solution is evaluated by the modified Crump method. Field geothermal property data are used to simulate the temperature distribution in an ATES system. The results show that the heat transfer in the aquifer is fast and has a vast effect on the vicinity of the wellbore. However, the aquifer temperature decreases with increasing radial and vertical distances. The temperature in the aquifer may be overestimated when ignoring the effect of thermal conductivity. The temperature distribution in an ATES system depends on the vertical thermal conduction in the rocks and the horizontal advection and thermal conduction in the aquifer. The present solution is useful in designing and simulating the heat injection facility in the ATES systems. Copyright © 2010 John Wiley & Sons, Ltd.