The large-scale development of shale gas is vital for enhancing energy security and driving regional economic development, yet systematic studies on the potential pollution risks associated with shale gas extraction activities in karst regions remain scarce. This study, focusing on the Fuling shale gas extraction area in Chongqing, investigates heavy metal concentrations and their spatial distribution in soil and groundwater during April to June 2024. It aims to identify potential sources of heavy metals and assess their environmental impacts. Through source apportionment and pollution risk assessments, the study clarifies the contribution of shale gas extraction to changes in heavy metal concentrations in both soil and groundwater and evaluates the associated pollution risks. The findings reveal that while most heavy metals in the soil and groundwater do not show significant exceedances, slight exceedances of Cd, Pb, and As were observed in the soil. Notably, Ba and Sr exhibited substantial enrichment and high spatial variability, with the average Ba concentration in soil reaching 561mg/kg, nearly twice the regional background level. The pollution indices for Ba, Sr, Cd, and Cu in soil were 3.08, 2.07, 1.42, and 1.21, respectively, indicating that shale gas extraction plays a key role in the accumulation of Ba and Sr in the environment. Furthermore, strong correlations (0.84, 0.78, and 0.76) between Cu, Sr, and Ba in both soil and groundwater suggest a common source for these metals. Source apportionment using APCS-MLR and PMF models revealed that agricultural, natural, shale gas extraction, and industrial sources contributed 17.1%, 28.1%, 15.4%, and 39.4% of the heavy metals in the soil, with shale gas extraction accounting for 50.9% and 47.4% of the Ba and Sr concentrations. In groundwater, shale gas extraction contributed 14.6% of the heavy metal concentrations, with Ba contributing as much as 30.3%. Overall, while the pollution levels in the soil-groundwater system of the Fuling shale gas extraction area are relatively low, the localized enrichment of Ba and Sr presents potential ecological risks. These findings provide a scientific basis for environmental monitoring and risk management of shale gas extraction in karst regions.