The earliest observations that Amazonian rivers can limit species distributions were made by Wallace in 1852. Two centuries later, the role of major rivers as drivers of biogeographic patterns in Amazonia is still a matter of debate. The effects of rivers as barriers for species dispersal can be expected to vary according to both species traits (such as body size and diet) and the characteristics of rivers themselves (such as flow rate, channel width, geological age, geomorphology, and floodplain dynamics). For example, the cumulative barrier effect of young rivers experiencing a dynamic history is expected to be less pronounced than that of old rivers coursing through stable channels. The evolution of river basins can therefore have a profound impact on the biogeography of the surrounding biota. We used data from standardized bird surveys to compare upland bird assemblages between opposite banks of two contrasting major Amazonian rivers. The Juruá is a highly meandering river carrying high sediment loads and draining the Solimões sedimentary basin, whereas the Tapajós is an entrenched river with low sediment load that runs through the cratonic area of the ancient Brazilian shield. Our objective was to investigate dissimilarities in species composition across each river and relate them to each river's characteristics and history. We found significant differences in bird assemblages between the opposite margins of the stable Tapajós, but not the more dynamic Juruá. This supports the notion that rivers experiencing a more dynamic history exert a weaker geographic barrier effect, and that geomorphological setting and landscape history are important determinants of the effect of Amazonian rivers on the dispersal and diversification of Amazonian vertebrate taxa.