The biodiversity and productivity of the Amazon floodplain depend on nutrients and organic matter transported with suspended sediments. Nevertheless, there are still fundamental unknowns about how hydrological and rainfall variability influence sediment flux in the Amazon River. To address this gap, we analyzed 3069 sediment samples collected every 10 days during 1995–2014 at five gauging stations located in the main rivers. We have two distinct fractions of suspended sediments, fine (clay and silt) and coarse (sand), which followed contrasting seasonal and long-term patterns. By taking these dynamics into account, it was estimated, for first time, in the Amazon plain, that the suspended sediment flux separately measured approximately 60% fine and 40% coarse sediment. We find that the fine suspended sediments flux is linked to rainfall and higher coarse suspended sediment flux is related with discharge. Additionally this work presents the time lag between rainfall and discharge, which is related to the upstream area of the gauging. This result is an important contribution to knowledge of biological and geomorphological issues in Amazon basin.