Both the smelter and acid mine drainage (AMD) in uppermost streams impact water geochemistry and deteriorate water quality. Efficient water quality management requires identifying the contribution of each source to stream water geochemistry. In this study, we aimed to determine the natural and anthropogenic sources (AMD and smelting) affecting water geochemistry by considering seasonality. Water samples were collected, from May 2020 to April 2021, in a main channel (Nakdong River) and tributaries in a small watershed including mines and smelters. The watershed is characterized by a carbonate-rich area in the upper-middle reaches and silicate-rich area in the middle-lower reaches. On the plots of Ca/Na vs. Mg/Na and 2(Ca + Mg) vs. HCO3 + 2SO4, the water geochemistry was predominantly explained by the carbonate and silicate weathering associated with sulfuric and carbonic acids. According to typical δ15N values for sources, nitrate contribution from soil-N mainly impacted water geochemistry, regardless of seasonality; the contribution from agricultural activity and sewage was negligible. Water geochemistry in the main channel samples was discriminated before and after passing through the smelter. The effects of the smelter were evident in elevated SO4, Zn, and Tl concentrations and in δ66Zn values; this was further supported by the relationships between Cl/HCO3 and SO4/HCO3 and between δ66Zn and Zn. These results were pronounced during winter, when the flush-out effect was absent. Our results suggest that multi-isotopes and chemical composition analyses can trace multiple sources influencing the water geochemistry in watersheds containing AMD and smelters.