An extremely high sulfate content is one of the main reasons for the deterioration of karst water quality in the Xin′an Spring area. Identifying the source of sulfate is of great significance for fully understanding the hydrogeochemical process in karst water and for the rational development, utilization and protection of karst water resources. In this work, the source of sulfate in karst water from the Xin′an Spring area is identified by sulfur and oxygen isotope. These results show that the sulfate in karst water mainly comes from gypsum dissolution, surface water leakage and pit water infiltration, and gypsum dissolution and mixing with surface water is the majority. This study provides important environmental and hydrogeological information for the protection, rational development and utilization of karst water resources in the study area.