This paper introduces the scientific part of a large-scale study in the Upper Peninsula (U.P.) of Michigan, a historical mining area, for exploring the water in deep abandoned copper mines as a geothermal energy resource. The main focus of the paper is placed on the scientific understanding of the natural mine water-geologic formation system, especially the transport of heat and mass in this large-scale natural system, which is critical to the efficiency and sustainability of the energy renovation. For this purpose, a field study involving measurements of temperatures and chemicals in a local mine shaft in the U.P. is conducted to reveal the major issue in recovering geothermal energy in the water from the shaft, i.e., the temperature distribution. Water samples are also collected in situ to investigate the distribution and concentrations of major chemicals. Afterward, a theoretical framework for the thermo-hydrodynamic process in the mine water coupled with heat transfer in the surrounding geologic formations is developed to outline a mathematical description for studying the scientific issue. Simulations are finally conducted, based on the real geologic information, to preliminarily investigate the quasi-equilibrium water movement in this local mine shaft due to geothermal gradients to provide insights into the phenomena observed in the field study.