The geochemistry of dissolved trace elements (V, Mn, Co, Ni, Cu, Zn, As, Rb, Sr, Mo, Cd, Sb, Cs, Ba, Pb and U) in the Upper Madeira basin, which constitutes the Bolivian part of the Amazon basin have been investigated. Using a statistical method (principal component analysis), the combined use of these geochemical data together with geological information on each watershed demonstrated the fundamental control of the substrate lithology on the trace chemistry of unpolluted surface waters within the catchment, at least in the Andean part of the basin. Three factors account for 87% of the variance. The first factor represents the influence of solution of evaporite and associated deposits occurring in the Andean Palaeozoic and Cretaceous sections; the second represents the influence of the mining activities being carried out in the Taquesi basin; and the third, the influence of black shale products and arenaceous-argillaceous rocks. In spite of the occurrence of evaporite rocks in the Upper Madeira watershed which tend to mask the trace-metal signatures of other lithological formations, it has been possible to discriminate the sources of trace metals present in the Andean and Amazonian Plain rivers.