The sediment, which is made up of soil, clay, and rocks, is what gives the water its muddy brown color. According to NASA, 1.3 million tons of sediment make the journey across the Amazon River to the Atlantic Ocean every day.

The "murkiness" of the Amazon River varies dramatically depending on which branch you are navigating, as the system is famously a "meeting of waters." The main stem of the Amazon is a "whitewater" river, which is actually an opaque, muddy ochre color due to the massive amounts of suspended sediment (silt and clay) it carries down from the Andes Mountains. In these sections, visibility is often less than 12 inches (30 cm). In contrast, tributaries like the Rio Negro are "blackwater" rivers; they appear like dark tea or coffee because of dissolved tannins from decaying jungle vegetation. While the water looks "inky" from the surface, it is chemically very clean and has much better clarity (up to several feet) than the main muddy channel. When these two types of water meet near Manaus, they flow side-by-side without mixing for several miles—a phenomenon known as the "Meeting of Waters"—creating a stark visual contrast between the "murky" silt and the "clear" but dark acidic water.