To understand the effects of atmospheric sulfur (S), nitrogen (N), and heavy metal (HM) deposition on streamwater chemistry in Buha River (BHR), the upstream of Qinghai Lake (QHL) on Qinghai−Tibet Plateau (QTP), water, mosses, and soil were collected from three representative small watersheds. Mosses had low S contents (0.09 ± 0.05%), slightly high N, zinc (Zn), and lead (Pb) contents (1.36 ± 0.46%, 78.7 ± 19.4 mg•kg −1 , and 10.5 ± 0.83 mg•kg −1 ), and quite high copper (Cu) contents (27.3 ± 4.65 mg•kg −1 ), compared with the global background values. The δ 15 N in mosses and soil Pb isotopic composition revealed the contribution of coal combustion to soil pollution via atmospheric deposition. The average SO 4 2− and NO 3 − concentrations of streamwater were 21.9 and 1.74 mg•L −1 . Elevated concentrations and increasing ratios of SO 4 2− /Cl − and NO 3 − /Cl − compared with historical levels indicated a significant impact of atmospheric deposition. However, the average Zn, Pb, and Cu concentrations in streamwater were 6.99 ± 2.36, 0.52 ± 0.87, and 2.22 ± 1.50 μg• L −1 , respectively, with very limited effects of HM deposition. The high pH of streamwater provided by the chemical weathering of carbonate rocks prevented water acidification and transport of HMs from soil to surface waters. Given QTP's ecological fragility and potential climate changes, the significance of long-distance atmospheric transportation to surface water still mattered.