The area is geographically diverse, consisting of grasslands bordering the Andes, gorges, and plains where climate is more variant and drier. The oxbow lake itself contributes areas of marsh and brushland. This is a nutrient-rich site, the soil consisting of silt and sand, and turnover along the riverbank occurs generally within 1000 years. The annual rainfall average is somewhat over 2000 mm, most of this falling from November to May. A marked dry season is from June to August. These factors combined lend to a relatively rapidly changing landscape.
Those areas which lie outside the path of the Rio Manu's meandering edges have vegetation much older than those closer to the river, but due to common treefall, the forest canopy is low. Much of the forest is only 25–30 meters tall, with a number of trees extending outside this range at 50 meters tall or more. An extensive network of lianas extends across the understory. Patches of bamboo, totaling almost a third of the locality, are marked by a scarcity of trees.
Along with La Selva Biological Station in Costa Rica and Barro Colorado Island (BCI) managed by the Smithsonian Tropical Research Institute (STRI) in Panama, Cocha Cashu is one of the best-studied ecological sites in the tropics. However, unlike La Selva or BCI, Cocha Cashu is in an area minimally impacted by humans, surrounded by millions of hectares of virgin forest, and thus provides critical insights into the organisms and processes found in a healthy, natural tropical rainforest. Over 500 articles, books, and other publications have resulted from field research conducted at Cocha Cashu. Studies related to those done at Cocha Cashu has been conducted at nearby Pakitza, on the same bank of Rio Manu, 21 km ESE. The two areas are very similar in makeup, reside at nearly the same elevation, and are not disconnected to impede species movement.
The Rio Manu area, in 1990, was found to consist of 1,856 species of vegetation, in comparison to the 2,874 species found in the entire national park. Much of the forest is dominated by trees and shrubs, rather than having a considerable population of epiphytes and terrestrial herbs. It is thought that this inequality may be due to either lack of intensive collection of these smaller flora, or due to scarce precipitation outside of the rainy season. Leguminosae (legumes) is the outstanding family of flora species makeup, with over 90 species. Moraceae, Rubiaceae, and Pteridophyta follow, with over 50 documented species each. Although no particular species of flora found at the Manu site was considered endemic to the area in 1990, it was suggested that the rate of forest loss might soon have created endemism. Annual production of seeds and fruit is high and well supports the site's animal communities. It has been considered that this may be in some significant part due to the prevalence of strangler figs, which make up a high proportion of the taller trees embedded within the canopy.
While the uncovering of the bird community dynamics of this area of the Amazon lagged behind other Amazonian sections, Cocha Cashu is considered a center of avian endemism (as identified by Haffer in 1985). Mist-net sampling of the bird populations at the site began in 1973, and by 1990, data on 435 regularly occurring species had been collected. Insectivorous species dominate overall with 163 species, though many of these appear in the understory. Birds with a near-exclusive fruit diet numbered 58, occurring most often in canopies along with omnivores. Common species include hummingbirds, manakins, and trumpeters.