The standing column well for ground source heat pump systems is a promising technology with high efficiency and environmental benefit, where groundwater is drawn from the bottom of a well and then re-injected to its top after transferring heat with heat pumps. Heat transfer analysis of the ground and aquifer involves complex problems in such a case. Determining the groundwater seepage flow is a precondition to solve the energy equation describing the heat transfer of the system. Only when piezometric head is obtained, the seepage velocity can be determined according to Darcy's law. This paper studies the groundwater seepage flow in an axial symmetrical geometry with the assumption that gross groundwater flow is neglected. An analytical solution of the groundwater seepage flow for a confined aquifer has been acquired by the integral transform method, which may provide a foundation for heat transfer analysis of the standing column well system.