The Tonle Sap floodplain’s size, habitat diversity, and relative preservation are of exceptional importance. The ecosystem is essential to the survival of many globally significant species of birds, mammals, and reptiles found around the lake during migration.

Flora. The flooded forest of the Tonle Sap is the largest remaining example of this type of habitat in Southeast Asia. It is a diverse unity of habitats, including shrub lands, stunted swamp forests, gallery forests, and submerged and floating aquatic vegetation. About 200 plant species have been recorded and the flora as a whole is distinct from that of other wetlands associated with the Mekong River, especially with regard to woody species. Some restricted-range tree species are endemic to the Tonle Sap and the southern coastal zone of Cambodia and have suffered from exploitation for charcoal production.

Fish. The fisheries of the Tonle Sap and the Tonle Sap River account for 15–20% of freshwater capture fisheries in the lower Mekong Basin and represent 50–70% of the catch for Cambodia. The fisheries productivity of the lake is known to be one of the highest in the world. This productivity is generally attributed to the flooded forest. A total of 107 fish species has been recorded for the lake only; the number of fish species living in the Tonle Sap River is probably higher, and new species are regularly discovered and described.

Invertebrates. Invertebrates are an important component of the Tonle Sap’s ecosystem. The available taxonomic information is incomplete but studies so far have identified 46 species of zooplankton. The rich biodiversity of mollusks in the Tonle Sap has been described as striking and 57 species of benthic invertebrates have been identified. Boeng Tonle Chhmar and the Stung Sen River and Sangke River estuaries are areas with high concentrations of bivalves. Three species of bivalves, two species of prawns, and one species of crab have been confirmed for the Tonle Sap. These freshwater invertebrates are an important source of food for people and aquatic wildlife.

Mammals. Some 46 mammal species are likely to occur in the Tonle Sap region. Some large species such as the Asiatic elephant and tiger used to migrate from upland areas to the Tonle Sap through natural corridors.
Cutting of the forested areas above the floodplain to make room for agriculture is now rampant.. This isolation has resulted in a decrease in the number of mammal species occurring in the Tonle Sap. The status of the mammal species that directly depend on the Tonle Sap is poorly documented, but they number at least 15 species.

Birds. The Tonle Sap (mainly at Prek Toal, but also at Boeng Tonle Chhmar) sustains the largest colonies of water birds in Indochina. Its floodplain is an important breeding area for ducks, jacanas, bustards, rails, herons and egrets, cormorants, darters, ibises, pelicans, and storks. Some 225 species of birds have been recorded in the Tonle Sap region since the 1960s.

Reptiles and Amphibians. The occurrence and distribution of amphibians and reptiles in Cambodia are not known well and herpetologists still rely on historical literature. There are probably 42 species of reptiles (including1 endemic water snake, 7 turtles or tortoises, and 1 crocodile).