The development of the transcontinental Amazon River System involved geological events in the Andes Chain; Vaupés, Purus and Gurupá arches; sedimentary basins of the region and sea level changes. The origin and age of this river have been discussed for decades, and many ideas have been proposed, including those pertaining to it having originated in the Holocene, Pleistocene, Pliocene, Late Miocene, or even earlier times. Under this context, the geology of the sedimentary basins of northern Brazil has been analyzed from the Mesozoic time on, and some clarifications are placed on its stratigraphy. Vaupés Arch, in Colombia, was uplifted together with the Andean Mountains in the Middle Miocene time. In the Cenozoic Era, the Purus Arch has not blocked this drainage system westward to marine basins of Western South America or eastward to the Atlantic Ocean. Also the Gurupá Arch remained high up to the end of Middle Miocene, directing this drainage system westward. With the late subsidence and breaching of the Gurupá Arch and a major fall in sea level, at the beginning of the Late Miocene, the Amazon River quickly opened its pathway to the west, from the Marajó Basin, through deep headward erosion, capturing a vast drainage network from cratonic and Andean areas, which had previously been diverted towards the Caribbean Sea. During this time, the large siliciclastic influx to the Amazon Mouth (Foz do Amazonas) Basin and its fan increased, due to erosion of large tracts of South America, linking the Amazon drainage network to that of the Marajó Basin. This extensive exposure originated the Late Miocene (Tortonian) unconformity, which marks the onset of the transcontinental Amazon River flowing into the Atlantic Ocean.