The sources, transport and storage mechanics, and contamination history of mercury (Hg) in the Madeira River, an important tributary of the Amazon River, were investigated from the Hg concentration and relevant geochemistry of flood plain and river sediment of one of its major Andean tributaries, the Beni River. Sediments containing clays and Al and Fe oxyhydroxides may serve as the primary carrier for Hg and facilitate its transport and storage within the Beni River-flood plain system. We estimate an annual exchange of clay-affiliated Hg between the flood plain and the channel of 2.1 t, due to channel migration, and a net Hg deposition of 2.4 t year-1, in the distal parts of the flood plain. Long-term records of sediment influx and efflux from the Beni foreland support this estimate of total Hg accumulation. Applying 210Pb geochronology to flood plain cores, we find that the clay-normalized Hg concentration in sediment was constant between 1900 and 1965, and then shows an increase over the past 30 years. This trend might be explained by the recent colonization, by a new mining boom in South America and by increased deforestation of hillsides and the resulting erosion of Hg-contaminated soils.