Environment protection is a core priority of many governments in this century. Most environmental problems have diverse causes: emission of greenhouse gases from fossil fuels, resource depletion, or intense mining activities such as the Huayuan manganese mine. The positioning of mining factories and water treatment stations impacts the surrounding groundwater reservoir. As the mine expands, the environmental impact also increases and the previous plan based on monitoring wastewater leakage has become inappropriate. Therefore, to solve this issue, a new study is required to understand the lateral resistivity distribution underground and to define a new station location for water treatment and divert the sewage to that station. In this study, the audio-frequency magnetotelluric method was used. Surveys of two long lines that cross the mining area to its boundaries were carried out. Data was robustly processed and inverted. Based on the inverted models in addition to geological information, drilling inspections, and solid waste distributions map, the integrated interpretation proposed two sites on the top of impermeable layers which constitute a buffer point between the unsafe (high concentration of pollutants) and the safe zones in the northwestern part of the mine. From the resistivity distribution combined with the water quality analysis, a relationship between fault structures reveals an interconnected conductive zone in the southeastern part. Being, the main channels for water circulating underground, these conductive zones delineate the main groundwater reservoir with a clastic aquifer layer. However, close to factories, water from faults contains solid wastes thereby making the groundwater in that zone non-potable, unlike the safety zone located in the northwestern part. To conclude, this workflow could become a field guide to improve the environment of mines and the deployment of hydrogeological drilling in a safe area.