To determine contamination sources and pathways, the use of multiple isotopes, including metal isotopes, can increase the reliability of environmental forensic techniques. This study differentiated contamination sources in groundwater of a mine area and elucidated geochemical processes using Cu, Zn, S–O, and O–H isotopes. Sulfate reduction and sulfide precipitation were elucidated using concentrations of dissolved sulfides, δ34SSO4, δ18OSO4, and δ66Zn. The overlying contaminated soil was possibly responsible for the contamination of groundwater at <5 mbgl, which was suggested by low δ65Cu values (0.419–1.120‰) reflecting those of soil (0.279–1.115‰). The existence of dissolved Cu as Cu(I) may prevent the increase in δ65Cu during leaching of contaminated soil in the sulfate-reducing environment. In contrast, the groundwater at >5 mbgl seemed to be highly affected by the contamination plume from the adit water, which was suggested by high SO42− concentrations (407–447 mg L−1) and δ65Cu (0.252–2.275‰) and δ66Zn (−0.105‰–0.362‰) values at a multilevel sampler approaching those of the adit seepages. Additionally, the O–H isotopic ratios were distinguished between <5 mbgl and >5 mbgl. Using δ65Cu and δ66Zn to support the determination of groundwater contamination sources may be encouraged, particularly where the isotopic signatures are distinct for each source.