River waters play a significant role in supplying naturally- and anthropogenically-derived materials to Lake Qinghai, northeastern Tibetan Plateau. To define the sources and controlling processes for river water chemistry within the Lake Qinghai catchment, high precision ICP-MS trace element concentrations were measured in water samples collected from the Buha River weekly in 2007, and from other major rivers in the post-monsoon (late October 2006) and monsoon (late July 2007) seasons. The distributions of trace elements vary in time and space with distinct seasonal patterns. The primary flux in the Buha River is higher TDS and dissolved Al, B, Cr, Li, Mo, Rb, Sr and U during springtime than those during other seasons and is attributed to the inputs derived from both rock weathering and atmospheric processes. Among these elements, the fluxes of dissolved Cr, B and Rb are strongly influenced by eolian dust input. The fluxes of dissolved Li, Mo, Sr and U are also influenced by weathering processes, reflecting the sensitivity of chemical weathering to monsoon conditions. The anthropogenic sources appear to be the dominant contribution to potentially harmful metals (Ni, Cu, Co, Zn and Pb), with high fluxes at onset of the main discharge pulses due, at least partially, to a runoff washout effect. For other major rivers, except for Ba, concentrations of trace elements are higher in the monsoon than in the post-monsoon season. A total of 38.5 ± 3.1 tons of potentially harmful elements are transported into the lake annually, despite human activities within the catchment being limited. Nearly all river water samples contain dissolved trace elements below the World Health Organization guidelines for drinking water, with the exception of As and B in the Daotang River water samples collected in late July probably mobilized from underlying lacustrine sediments.