This study describes the transport and speciation of mercury (Hg) and the associated role of organic matter in these processes at the confluence of the Negro (‘black waters’) and Solimões (‘white waters’) Rivers, which form the Amazon River. The Negro has the highest total Hg content (11·6 to 18·2 ng l−1) due to the extreme particulate Hg concentrations (2074 ng g−1 at the surface), 10 to 20 times higher than those measured in other Amazon tributaries. The total organic carbon (TOC) consists primarily of dissolved organic carbon, which corresponds to 89% and 66% of the TOC in the Negro and Solimões Rivers respectively, and is mainly composed of humic substances, carriers for most of the metal ions transported in rivers. At the confluence of the Negro and Solimões Rivers, the total Hg concentrations decrease markedly. An isotopic mass balance showed that the complete mixing of the two rivers was achieved 25 km downstream of the confluence. At 60 km downstream of the confluence, the flux of Hg decreases to 73 kg day−1, which represents a net losses of 5 kg day−1 and 15 kg day−1 of dissolved Hg and particulate Hg respectively, assuming that the discharge was constant during the sampling survey and without significant lateral input. Moreover, the Hg losses are correlated with the total suspended matter concentrations, which vary throughout the mixing zone, and also with the particulate and dissolved organic carbon distribution. We suggest that the dissolved loss occurs during the flocculation of organic matter within the zone of rapidly changing physical and chemical conditions downstream of the confluence, and that the particulate loss is by the deposition of particles along the mixing zone favoured by decreasing stream velocities during the sampling survey. Adsorption processes of Hg on dissolved organic matter seem to be responsible for the decrease of dissolved Hg concentrations in the mixing zone. Copyright © 2003 John Wiley & Sons, Ltd.