Both the Ucayali and the Marañón originate in the Andes Mountains; the Ucayali actually has its headwaters in the Urubamba River around Machu Picchu and Cuzco.

Rivers that come from the Andes are rich in sediments that they pick up as they tumble down the rocky mountains. This gives the rivers a whitish-brown color. As this nutrient-rich water flows through the flooded forests many of the sediments become deposited on the forest floor, and at the same time, the water becomes impregnated by dark tannins from the leaf litter – the same effect that tea has on water. When the water flows out of the forest and into the channels and lakes it has a dark, almost black color.

The rivers of the reserve have a particularly large population of river dolphins and is the last remaining refuge for the Amazon manatee. Giant river otters are also sighted in the rivers, lakes and channels. There are 13 species of primates in the reserve, many of which are commonly sighted on the forest walks. Macaws and wading birds are very abundant, as are game birds. Peccaries, deer, tapir and capybara are also found. The turtles have rebounded and are now common features of the rivers as are caiman. Here can still be found large black caiman.

The Pacaya-Samiria National Reserve is working with the local Cocama Indians to ensure that the natural and human worlds can coexist in harmony. While their dress has changed, the Cocama Indians still live as they did centuries ago. They fish and hunt for meat, collect forest fruits and have small slash and burn gardens. They travel in small dugout canoes and live in thatched roofed houses made from trees and palm fronds of the nearby forest.