The sulfate concentration of the water body in the Ziyang stone coal mining area exceeds the standard, and the pollution is becoming more and more serious. Identifying the source of sulfate pollution is extremely important for the prevention of pollution and the guarantee of drinking water safety. The production mechanism of acid wastewater was analyzed and identified using sulfate and oxygen stable isotopes. The results show that the sulfate produced by the sulfide oxidation of stone coal was the main source of sulfate in acid wastewater. Calculated by the IsoSource mass conservation model, the contribution rate of acid wastewater to groundwater sulfate is about 36.5%. The application of multiple isotopes provides a new approach for the comprehensive identification of sulfate sources in acid wastewater and the quantitative study of its impacts on groundwater and provides a scientific basis for mine development and ecological environmental protection and restoration.