This paper presents the method to simulate groundwater flow and heat transfer in complex hydrogeological conditions for standing column well (SCW) system, pumping and injecting groundwater in single borehole among ground source heat pump (GSHP) systems. The borehole is modeled to 1D discrete elements, aquifers are modeled to 3D elements by FEFLOW to simulate pumping, injecting and bleeding of SCW. In this paper, we analyzed effect of roughness of borehole and conductivity of dip tube for SCW by using FLUENT, and focused on groundwater flow and heat transfer in complex geological and hydrogeological conditions rather than turbulent flow inside borehole or heat conduction through dip tube. The results show that the model developed in this paper is consistent with experimental results. The geothermal heating and cooling system for a field problem was developed based on simulation results of SCW. (C) 2017 Elsevier B.V. All rights reserved.