The Yarlung Tsangbo (YT) is a large river running across southern Tibet and has significant effects on its lower reaches, the Ganges-Brahmaputra Basin. In order to investigate the geochemical features of the YT, 18 surface sediment samples were collected; ten trace element concentrations were measured for bulk sediments and two fine grain size fractions. Meanwhile, basic physicochemical parameters and element concentrations of river water were also analyzed. Results indicated that the river water was alkaline (pH 8.42) and that dissolved oxygen was mainly controlled by river water temperature. Some elements (e.g., Zn and Ni) showed close negative relationship to mean grain size of the sediments. Concentrations of most heavy metals, except As of the YT bulk sediments, were similar to those of Upper Crustal Concentration and its lower reaches, indicating almost no anthropogenic impact. Arsenic of the YT sediments was derived fundamentally from the parent rocks of the YT Basin and was far higher than that of its lower reaches. This indicates that relatively small amounts of As from the study area were transported down to the Brahmaputra River under present, relatively dry climatic conditions. However, more YT sediments might have been transported to its low reaches during the Holocene due to the wet climate, giving high As concentration in Holocene sediments of the Ganges-Brahmaputra Basin. Thus, As transported by the YT may produce important influence on the Ganges-Brahmaputra Basin and contribute to its high As concentration in groundwater.