Nickel (Ni), copper (Cu), and zinc (Zn) are commonly used in human activities and pollute aquatic environments including rivers and oceans. Recently, Ni, Cu, and Zn isotope ratios have been measured to identify their sources and cycles in environments. We precisely determined the Ni, Cu, and Zn isotope ratios in rain, snow, and rime collected from Uji City and Mt. Kajigamori in Japan, and investigated the potential of isotopic ratios as tracers of anthropogenic materials. The isotope and elemental ratios suggested that road dust is the main source of Cu in most rain, snow, and rime samples and that some of the Cu may originate from fossil fuel combustion. Zinc in the rain, snow, and rime samples may be partially attributed to Zn in road dust. Zinc isotope ratios in the Uji rain samples are lower than those in the road dust, which would be emitted via high temperature processes. Nickel isotope ratios are correlated with V/Ni ratios in the rain, snow, and rime samples, suggesting that their main source is heavy oil combustion. Furthermore, we analyzed water samples from the Uji and Tawara Rivers and the Kakita River spring in Japan. Nickel and Cu isotope ratios in the river water samples were significantly heavier than those in rain, snow, and rime samples, while Zn isotope ratios were similar. This is attributed to isotopic fractionation of Cu and Ni between particulate-dissolved phases in river water or soil