The influence of mining activities on groundwater quality is a growing concern due to highly toxic metals in the tailings. Carbonate rocks are common in the surrounding rocks of ore deposits. But such mining districts generally do not have the conditions to construct traditional tailings impoundments due to the different degrees of karstification. This paper utilises field investigations, chemical analyses, and permeability tests, etc. to study the effect of tailings impoundments on the underlying karst water systems in the Gejiu world-class Sn-polymetallic mine located in a typical karst region in southern China, with samples collected from both karst springs deriving from the mining area and tailings porewater. Because of the abundance of sulphide minerals in the ores, acid mine drainage is expected to pose a high risk. However, the results indicate that the tailings porewater is moderately neutral and is characterized by the SO4–Ca–Mg hydrochemical type. This can be attributed to the substantial buffering capacity of carbonate minerals. Pollution elements in the tailings porewater mainly include SO42− and toxic metals including As, Cd, Mn, Pb, and Hg. The type of pollution factors and the degree of contamination are not consistent in the different tailings impoundments. The hydrochemical classification of four karst springs distributed in the south of the mining area is HCO3–Ca–Mg. The concentrations of SO42− and the toxic constituents in the springs are far below the national standards for drinking water. The spring water not being contaminated may be attributed to the operation mode of the tailings impoundments (peripheral discharge and reuse of ponded water), the residual clay between the tailings impoundments and the carbonate bedrocks and the sufficient buffering capacity of the underlying karst systems. The tailings disposal at the Gejiu tin mine within the natural karst depressions is able to provide a reference for the operation of karst mines in China and elsewhere.