Low-to-medium temperature geothermal fluids in the granite regions of southeastern China are an important renewable energy resource, but they are also a source of contamination containing highly toxic elements such as fluoride and arsenic. This study analyzed the origin of the geothermal fluids in a regional-scale hydrogeological unit in the city of Xiamen, China, based on isotope and hydrochemical analyses. The Br/Cl ratios suggested that the inland geothermal fluid is merely recharged by rainwater from the mountain edge, while the coastal geothermal fluid is originally recharged by the seawater and later mixed with rain-derived groundwater. The geothermal water featured high SiO₂ and detectable Zn concentrations. The former reflects the significant water–granite interaction along the flow path, and the latter indicates the active hydraulic connection between surface waters, shallow aquifers and deep geothermal fluids. High radon content was detected near the deep conductive fault adjacent to a geothermal well, demonstrating that the fault damage zone acts as a major conduit for upward transport of the deep geothermal fluid. As a result, the fault damage zones developed in the granite are necessary for the formation of geothermal water, which leads to the uneven distribution of geothermal water in the subsurface. High-temperature geothermal water can be found in those regions with fairly sparse fault damage zones. In contrast, in the region with high-density fault activities, the active communication between shallow cool water and deep geothermal fluids can decrease the water temperature.