The nature and distribution of organic matter in the mixing zone of black (Rio Negro) and white (Rio Solimões) waters in the Amazon River was studied to understand the processes responsible for its transport and distribution. Water samples from 13 stations, including Rio Negro, Rio Solimões and Rio Madeira and ten stations downstream of the confluence with the Amazon, were collected during a low-water period. Particulate organic matter (POM; >0·7 µm) and dissolved organic matter (DOM; <0·7 µm) were quantified by analysing elemental carbon and nitrogen and by high-temperature catalytic oxidation, and characterized by infrared spectrometry and fluorescence microscopy. We also performed adsorption experiments with DOM and alumina particles to determine the adsorption abilities and the nature of the most reactive DOM. Adsorption was estimated by measuring the amount of dissolved organic carbon (DOC) lost during the experiments. We found a significant difference between the measured and theoretical fluxes of the two end members in DOC (−52%), particulate organic carbon (−32%), and particulate organic nitrogen (−59%). This suggests that organic matter is not conservative at the confluence of the two rivers. Among processes affecting POM and DOM during the mixing of the two rivers, adsorption may be one of the principal mechanisms by which the dissolved fraction is removed. Adsorption experiments showed that up to ca 40% of DOC can be removed by adsorption reactions. Furthermore, dissolved organic nitrogen was preferentially adsorbed onto alumina surfaces, which may be important for the fractionation of organic matter in the Amazon river system and seems to be related to the origin and freshness of the DOM. Copyright © 2003 John Wiley & Sons, Ltd.