A hilly to mountainous watershed in Chonju in central Korea does not receive acid rain (average pH: 6.2); however, the stream water in the granite watershed is slightly acidic (6.4–6.7) and contains a low concentration of Ca compared to the stream water in sedimentary and volcanic rock watersheds (6.8–7.6). Although the concentrations of Ca and Sr and the 87Sr/86Sr ratio in the stream water change in accordance with the watershed geology, the stream 87Sr/86Sr ratios are closer to the 87Sr/86Sr ratios of rain than to those of the substrate rocks, suggesting the selective but sluggish weathering of Ca-containing minerals neutralizes acid. The concentrations of trace metals (As, Cr, Cu, Mo, Ni, Pb) in the water are lower than those in rain and less dependent on the watershed geology, indicating that they originated dominantly from the atmosphere. This result is consistent with the stream water having Pb isotope ratios close to that of rain but distinct from that of the rocks. We assume that the soil pool of exchangeable ions dominantly contains atmospherically derived heavy metals, which are subsequently discharged into streams. It is likely that the poor acid-neutralizing capacity of granite makes the aquatic systems in the granite watershed in Chonju sensitive to atmospheric acidification.