The chemical composition of the Amazon River results from the mixing of two water types: black water and white water. On-site fractionation by sequential tangential ultrafiltration (STUF) was used to differentiate transported organic carbon and to determine the distribution and association of major and trace elements with different size fraction of the organic carbon (OC). Several sampling campaigns (1994–1996) allow a monthly quantification of particulate (OCP, MeP), colloidal (OCC, MeC) and dissolved (OCD, MeD) organic carbon and metal ions inputs. In white rivers the OC is mainly concentrated in the low molecular weight fraction (OCD < 5000 D) while in black rivers most of the OC is in the heavier molecular weight fractions (OCP and OCC > 5 kDa). For Mg, Ca and K, 50% of the total amount of each element is found in fraction MeD while 15% and 35% are found in fractions MeC and MeP, respectively. Al and Fe are in the particulate fraction at 99% of the total metal concentration for all river samples. This work emphasizes the coagulation processes and the sink for elements in the mixing zone. These physicochemical transformations of the organic matter vary seasonally. The changes happen during the transition periods: before high-level waters and before low-level waters. By way of flux measurement, a seasonal carbon loss was observed. The estimated annual organic carbon flux of the Amazon at Òbidos is 28 × 106 t. At the same time, an average of 9 × 106 t of organic carbon per year is retained in the reach between Manaus and Òbidos, probably via coagulation processes. Copyright © 2003 John Wiley & Sons, Ltd.