Karst groundwater contamination has emerged as a worldwide environmental and health hazard. Karst aquifers, even for the buried karst systems, have strong contamination sensitivity and great pollution risk due to the good pipe fracture connectivity. The large burial depth and invisible hydrologic connectivity pose a challenge for the diagnosis of the contamination sources and identification of the contamination pathways of buried karst aquifers. To address it, a comprehensive application of hydrogeological and hydrogeochemical investigation combined with multiple isotopes (δ2H, δ18O, δ34S, δ13C and 87Sr/86Sr) were performed to elucidate the multiple contamination sources and migration pathways of contaminants in Jinci Spring, a complex buried karst water system. The results obtained highlight that the hydrological connectivity and source availability determine the specific contamination process in buried karst aquifer. Karst aquifer under the river channel is observed to be influenced by the vertical infiltration of polluted river water as indicated by elevated chloride levels (mean 79.4 mg/L) and higher δ2H (mean −8.8 ‰) and δ18O (mean −64.5 ‰) values. Evidenced by the excess of sulfate (mean: 1454 mg/L) and depleted δ34S (mean: −1.6 ‰), the lower karst aquifer may receive the leaking recharge of the mining waste water in the overlying coal seams. The occurrence of nitrate in karst water may be induced by reverse recharge from neighboring confined quaternary aquifers, indicated by the elevated nitrate concentration (15.0–50.8 mg/L) with high 87Sr/86Sr ratios (mean 0.7124). Our findings suggest that over-pumping of deep karst waters may produce additional pollution sources by altering the natural recharge relationship between montanic karst waters and the neighboring pore waters within the basin. Research in this paper improves our understanding of groundwater pollution and hydrological connectivity in buried carbonate aquifers and the protection of karst water resources.