To provide theoretical support for the protection of centralized drinking groundwater sources in karst areas, it is necessary to accurately identify the development of karst conduits and analyze the differences in hydrogeochemical characteristics of different karst systems. This provides a scientific basis for the accurate designation of risk zones that may cause drinking groundwater pollution. In this study, a geophysical survey, hydrogeological chemical process analysis and optimized fuzzy cluster analysis were used to gradually improve the understanding of karst water systems. AMT and HDR methods were used to calibrate the resistivity around the water-filling karst conduits, which ranged from 39 to 100 Ω·m. A total of seven karst systems were identified, including four karst systems in the north of the study area, one karst system in the west and two karst systems in the south. Analysis of the hydrochemical data showed that HCO3-Ca and HCO3-Mg-Ca types accounted for 90% of all samples. The δD and δ18O values of their main conduits were −51.70‰ to −38.30‰ and −7.99‰ to −5.96‰, respectively. The optimized fuzzy clustering analysis method based on the weight of variables assigned by AHP more accurately verified karst water systems. Based on these findings, the drinking groundwater source risk zone was designated with an area of 33.90 km2, accounting for 34.5% of the study area. This study effectively improved the rationality and accuracy of the designation of drinking groundwater source risk zones in karst areas, and provided a scientific basis for the identification of karst water systems and decision-making of drinking groundwater source protection in karst areas.