Bob Johnson: An overview of the geological history of the Amazon Basin
The Amazon basin is slightly larger than the continental U.S.; a rather large piece of land. Charles Darwin wrote three books on the geology of the Amazon, long before the theory of continental drift revolutionized geology in the 1960s. According to continental drift theory, about 500 million years ago (mya) the four southern continents were a single chunk of land, Gondwanaland. The land we know now as Manaus has always been near the equator, even as other continental plate action occurred. About 135 mya, the other continents collided with Gondwanaland to form a single supercontinent, Pangaea. After that the mid-Atlantic rift opened up and spread North and South America apart from Eurasia and Africa; this spread started in the north first, splitting North America off from South America and isolating South America from the other continents for most of the last 135 million years. When the South American plate hit the Pacific plate, the Andes formed due to subduction. Before this point, the water in the Amazon region flowed very slowly westward and drained into the Pacific, so the area was essentially a big brackish marsh; but as the Andes uplift progressed, the westward flow stopped and then reversed towards the Atlantic. For a long time a great deal of water was trapped by shields (the Guayana and Brazilian shields) to the east, creating a huge freshwater lake; this state of affairs lasted until about 23 mya. Even now, however, the Amazon basin is in a sense the largest inland body of water in the world; ships can sail all the way to Peru, and the difference in elevation of the water across the Amazon basin from the Atlantic to the border with Peru is only about 600 feet, so it can be viewed as a very large, marshy lake with an outflow to the Atlantic ocean. Today, sediment-rich waters from the Andes provide the "white water" of the Solimoes; nutrient-poor waters from the Guayana shield area color the waters of the Rio Negro.
During ice ages, water levels have fallen and the Amazon has turned into savannah; species survived in refugia at higher elevation, particularly in the western Amazon. At the end of each ice age, the water levels rise, the savannah floods, and species recolonized the area. The connection between North and South America through Panama formed some time between 3.1 (traditional estimate) and 1.8 (most recent estimate) mya; apart from migration via vegetation rafts and such, communication of species between the continents was limited before this occurred, although an island archipelago must have formed between the continents somewhat earlier, and some birds and insects could migrate between continents all along.
In summary, the Amazon basin has always been near the equator, has always been essentially flat, and has had a great deal of unique flora (no flowering plants) and fauna (marsupials) due to its isolation.