Being a geologist from principle, I could not resist myself to have a look into literature on the paleo-Amazon. This information will help in the understanding of the Amazon vegetation structure nowadays. Perhaps even to understand future trends, although these future trends that we tend to predict have a very different time scales.
Initially the Amazon did not flow from west to east
The first indications of the Amazon River can be found back some 40 million years ago, during the Paleogene. The recently formed Andes and the existing high-topography shields of Guyana and Central Brazil formed a huge interior sea, in which the headwaters of the Amazon formed. This was the so-called Pebas basin (lake) and coincided with the current dense rainforest of the western Amazon region. In this basin, a network of smaller rivers was formed, which we might better categorize as being tributaries of the paleo-Orinoco. In those times, the Amazon did not flow to the east, but instead followed a route north draining into the present-day Gulf of Mexico. For a long time, the Pebas basin was a huge drainage pot for its surrounding mountains (Andes and Guyana Shield), and functioned like a kind of extension of the Gulf of Mexico. From the Gulf, sea level fluctuation, resulting climate change, induced the occasional flooding (incursions) and draining of the basin, forming the lacustrine (lake) sediments nowadays found in the western Amazon. The real Amazon was only a minor river draining on the west side of the Guyana shield.
During the Miocene things changed. We are jumping to approximately 20 million years ago. World-wide temperatures were decreasing from a very hot climate to a more temperate climate (similar to present-day). Meanwhile, the uplifting of the Andes continued rapidly and mountain ranges formed in the northern part of Latin America (Venezuela and Colombia). The Pebas basin was slowly cut off from its drainage point in the Gulf and the Amazon experienced more resistance to flow in that direction. Searching another route, the Amazon River cut itself loose from the Orinoco River and moved eastward. The Pebas basin developed into a large inland wetland, vegetated mainly with palm swamps and lowland riverine forest. Only at the end of the Miocene, some 10 million years ago, the river managed to breach through the so-called Purus Arch and connected to the much smaller eastern Amazon River. This break-through must have forced a violent burst and ecological disasters. In the fan delta of the current Amazon River,we find a sharp change in its sedimentary succession from this time onwards with significantly higher sedimentation rates. During the first couple of million years, the Amazon River is still not well developed and the Pebas wetland coexisted along with the river draining it.
Fluctuations during ice ages
In the Pliocene (around 5 million years ago), ice ages started to appear. The era of ice ages meant a rapid fluctuation in temperature, rainfall and sea level. The waxing and waning of polar ice caps did not just happen once, but many times. During this phase the Amazon River developed to its present form, incising deeper and deeper into the gorge, which it had formed by connected east and west breaking through the Purus Arch. Swamps and lakes still persisted, and flooding events due to reformations of the river course were common. Only since the last ice age the current Amazon River channel along Manaus formed: 5,000 to 2,500 years ago major flooding events occurred establishing this flow channel. This was while the Romans conquered the old world.
Thus, although the Amazon river nowadays seems to be a very stable river, it did not always exist in the way we know it and it shows to be a living and moving system.
Some papers on the Miocene river reversal: Hoorn, C.; Guerrero, J.; Sarmiento, G.A.; Lorente, M.A. (1995); Andean tectonics as a cause for changing drainage patterns in Miocene northern South America; Geology 23 (3); p. 237-240 & Figueiredo, J.; Hoorn, C.; Ven, P. van der; Soares, E. (2009); Late Miocene onset of the Amazon River and the Amazon deep-sea fan: Evidence from the Foz do Amazonas Basin; Geology 37; p. 619-622
A paper on the Holocene Amazon: Fatima Rossetti, D. de; Toledo, P.M. De; Goes, A.M. (2005); New Geological framework for Western Amazonia (Brazil) and implications for biogeography and evolution; Quaternary Research 63; p. 78-89