Each of the Amazon's thousands of tributaries starts at a high point—either in the Andes, the Brazilian Highlands, or the Guiana Highlands—and then steadily loses elevation and picks up speed until it begins to approach the Amazon Basin. Scientists have divided these tributaries into three broad categories—milky, black, and clear—in reference to the color that they take on while carving their way through three different types of terrain. Alfred Russel Wallace, British naturalist and friend of Henry Walter Bates and Charles Darwin, made the distinction widely known in the mid-nineteenth century when he published his Narrative of Travels on the Amazon and Rio Negro. Wallace noted the striking difference between the milky Amazon and the black waters of the Negro where they collide on the northern bank of the Amazon. Seen from above, the meeting of these two colossal rivers looks like black ink spilling over parchment paper. The visual effect is heightened because the Negro, which is warmer and thus lighter in weight, rides on top of the Amazon, and the rivers do not fully blend until they have traveled dozens of miles together downstream.SOURCE: The River of Doubt: Theodore Roosevelt's Darkest Journey, by Candice Millard (Doubleday, 2005), pp. 171-173
Milky rivers, such as the Amazon and the Madeira, generally have their origins in the west and are clouded by the heavy sediment load that they carry down from the youthful Andes. Blackwater rivers, on the other hand, usually come from the ancient Guiana Highlands in the north and so wash over nutrient-poor, sandy soils. Scoured by millions of years of hard rains, these soils cannot retain decomposing organic matter—mostly leaves—which, when swept into a river, literally stains the water black like tea.
Although during the rainy season the River of Doubt is nearly as black as the Negro and as murky as the Amazon, it is technically a clearwater river. Like the Amazon's largest clearwater rivers, the Tapajos and the Xingu, it has its source in the Brazilian Highlands, and so it picks up very little sediment as it flows over ancient and highly eroded soil. Clearwater rivers are also less acidic than blackwater rivers. Some, most notably the Tapajos, are so clear that they look blue, perfectly mirroring the sky above them. But most, like the River of Doubt, mix with either blackwater or milky tributaries as they snake through the rain forest, and so look neither blue nor clear by the time they reach their mouth.