Studying the influence of shale gas exploration and development on groundwater environment is the basis of guiding water environment protection in the process of shale gas exploration and development. Groundwater environmental pollution is concealed, complex and persistent. Once it is difficult to control the pollution, the current commercial shale gas development zones in Sichuan Basin that are mostly located in karst areas and highly sensitive to groundwater will be vulnerable to the impact of shale gas exploration and development. Based on the hydrogeological conditions of shale gas exploration and development area and combined with engineering analysis of exploration and development, various risk pathways that may affect the groundwater environment during process of shale gas exploration, mining well construction, mining operations and other stages were identified in this paper. Some existing risk pathways were proved by verification of typical areas and should not be ignored. Based on the actual situation of typical areas, the countermeasures of groundwater environmental protection in the process of shale gas exploration and development in karst areas were discussed. It is believed that the groundwater environment can be better protected by strengthening administration, research and application of new technologies, precise design, hydrogeological conditions, and research and feedback of groundwater environmental protection.