Water and suspended sediment fluxes are considered during the period 2000-2008 in a region including the full Amazon River from the confluence of the Negro River to Santarem, the end part of the Solimoes River, and the lower part of the Madeira River. Three types of data are used: water discharge estimated from field measurements, and suspended sediment obtained from field measurements and derived from MODIS satellite data. A generalized least square method including a propagating term is developed in order to propagate the signal upward and downward the river. The approach is introduced and tested. Several experiments are considered in order, first, to estimate the ability to propagate the signal from stations located before the confluences of Negro and Madeira Rivers to stations located on the Amazon River; second to investigate the possibility to propagate the signal along the Amazon River which dynamics is coupled with floodplains dynamics; and third to produce optimal solutions of water and sediment fluxes. For each experiment, the influence of field and satellite data is compared. The approach is efficient in the upper part of the region of study where the Solimoes, the Negro and the Madeira Rivers meet and fails in the lower part of the region where interactions between Amazon River and floodplains play an important role on the fluxes' dynamics. The optimal experiment includes in situ and satellite data from all the stations available and is used to analyse the recent evolution of suspended sediment flux along the Amazon River and its interaction with the large coupled floodplains. A high accumulation rate is observed during the 2000-2002 period, followed by decreasing rates until 2005 and by increasing values in 2006 and 2007. Our results suggest that floodplains extending along a river reach of 390 km-long between Itacoatiara and Obidos trap about 15% of the suspended sediment flux passing at Obidos. The simulated deposition rate is of about 0.3 Mt km(-1) yr(-1) corresponding to an accretion rate of about 27 mm yr(-1).