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Forest clearing through slash and burn to open up agricultural land is an ongoing process in large parts of the Amazon Basin. This activity severely affects the structure and balance of the natural ecosystem, and also has the potential to cause substantial changes in landscape geochemistry. The latter is the topic of this study, with special attention on translocation of potentially toxic trace elements from deforested areas to downstream aquatic and terrestrial systems. Sampling of floodplain sediments and mountain soils (Inceptisols on redbed lithologies) was carried out in two adjacent Subandean river basins, with deforestation extents of ca. 1/3 and 2/3 of the basin areas. Several toxic and potentially toxic metals (e.g., Hg, Cd, Pb, Cu and Ni) and other major and minor elements showed concentration peaks at certain depths in the alluvial deposits of both basins. These peaks were associated with organic matter, and occurred just below layers of combustion residues originating from burning of in situ biomass. Downward migration of particles originating in the combustion residues is suggested to be the direct mechanisms of the metal enrichments. Further evidence of an in situ origin of the metal peaks in the sediments was provided by the geochemical composition of soils located upstream of the floodplains. Disturbed soils (i.e. soils of pasture, coffee plantations, secondary forest and recently swidden fields) were found to be similar to soils under natural forest. Moreover, trace element concentrations in floodplain deposits were similar in the two drainage basins despite the large difference in exploitation degree. Thus, no evidence was found of large scale (basin-wide) increases in trace-metal leaching or translocation as a result of the extensive deforestation and agricultural land-use that has been practiced in the Amazonian highland jungle over more than 100 a.