The distribution of trace elements (Sr, Mo, Ba, Rb, U, Mn, Ni, Cu, Zn, and Cd) was investigated in surface waters and associated particulates in two upper Amazonian basins (Mamore and Beni). Dissolved Sr, Ba, Mo, Rb, U and to a lesser extent Zn and Cd correlate with major ions and appear to be predominantly derived from soluble rocks (carbonates, evaporites or sulfides essentially contained in shales). These elements are conservative in waters except in highly alkaline or sulfate-rich waters where calcite and barite can precipitate. The concentrations of transition element are generally not correlated with major ion chemistry. Their behaviour can be largely explained by equilibrium reactions in solution and solid–liquid exchanges. Additionally, the distribution of Mn and Cu reflects also the lithological differences between the Mamore and Beni basins. The occurrence of mineralisation in the Beni basin explains the high Zn, Cd as well as the concentrations of Cu in some rivers of the Beni basin. The higher content of Mn in the Mamore basin may reflects the predominance of carbonate rocks. The fractionation of trace elements in SPM has been attributed to the sorting of feldspars during transport in water, and to the mixing between clay minerals and quartz. These minerals, refractory to weathering and introduced in water rivers by mechanical erosion, have not contributed to the dissolved load.