The Amazon River is the mainstem of the world's largest fluvial system. Despite the common idea that the Amazon River flows in a remote region, about 20 million people live scattered in its rivers margins in Brazil. The presence of microplastics in riverbed sediment samples collected in seven sites from Solimões, Negro and Amazon rivers, upstream and downstream the metropolitan region of Manaus was investigated. Concentrations ranged from 417 to 8178 parts/kg sediment dw (microplastics: 0.063–5 mm), and from 0 to 5725 parts/kg sediment dw (microplastics: 0.063–1 mm). The highest microplastics concentrations were observed in samples from shallow water (water depth of 5–7 m) sites with lower water velocity of the Negro river surrounding Manaus, and the lowest concentration in farthest sample collected in deeper zone (water depth of 34 m) of the Amazon river around 110 km downstream Manaus. The variation of microplastics concentrations within the studied area can be related to hydraulic characteristics defining the erosive-depositional behavior of the sampling sites and their proximity to Manaus. The sediment samples of the Negro river near Manaus presented the higher microplastic concentrations, probably due the combine effects of hydraulic conditions suitable for sediment accumulation and proximity to the urban area of Manaus. The lower concentrations of microplastics in the Solimões and Amazon rivers are attributed to their more erosive and bypassing hydraulic conditions, especially in deeper zones near the thalweg. These results are the first report to show the ubiquitous presence and widespread distribution of microplastics in sediments from the lower Solimões, lower Negro and upper Amazon rivers. The presence of microplastics in sediments from the largest Amazonian rivers points out that we must advance our knowledge about sources and fate of microplastics to infer their impacts on Amazon ecosystems.