The Himalayan valleys are important transport channels of atmospheric pollutants from South Asia to the Tibetan Plateau. This study aims to demonstrate the use of biomonitors (i.e., tree foliage, bark, mosses, and lichens) in the Himalayas to understand the sources and accumulation of mercury (Hg), including the transboundary atmospheric Hg transport across the Himalayas. Results showed that the significant variability in the physiological characteristics and nutrient uptake pathways, coupled with rapid changes in topography and climate-forced precipitation, led to significant differences in concentrations and isotopic compositions among biomonitor species. Δ199Hg values (−0.32 to −0.10‰) at the lower altitudes were slightly more positive than values at upper altitudes, likely reflecting signals of transboundary transport of anthropogenic Hg from South Asia. The isotope mixing model determined atmospheric Hg0 as the main source of Hg in most biomonitors (67 ± 13% to 88 ± 13%), except for Usnea longissimas (i.e., a unique type of lichen) with 61 ± 16% contribution of atmospheric Hg2+. Additionally, the morphological structure and epiphytic environment of U. longissimas facilitate aqueous Hg secondary reactions. Our results suggest that the Hg cycling in the Himalayan valleys could mix multiple impacts from montane environments and signals of transboundary transport of anthropogenic Hg from South Asia.