Kaludiya Pokuna is also rich with numerous biodiversity, both flora and fauna. The forest is home for many endemic and non-endemic species of flora and fauna, that prevail much more secure than other forests in Sri Lanka.

Site is surrounded by farmland and human settlements from the north, east, and west but is undisturbed by humans and the primates are not provisioned. There is no evidence to indicate that hunting, timber extraction, or woodcutting have occurred at the site.

Forest is composed of many endemic and highly valuable trees and shrubs. The majority of flora are in the family Euphorbiaceae. Plants like Hydnocarpus venenata, Mischodon zeylanicus, Lepisanthes senegalensis, Grewia rothii, Ficus microcarpa, Mussaenda frondosa, Drypetes sepiaria, Mallotus eriocarpus, Manilkara hexandra, Dimocarpus longan, and Tetrameles nudiflora are abundant. Plants of family Ebenaceae, such as Diospyros ebenum, Diospyros malabarica, Diospyros oocarpa, and Diospyros ovalifolia, which has large timber value, are enormous without any human conflict.

Kaludiya Pokuna is rich with its populations of primate species mainly, where many researches on primates based on this site, especially on tufted gray langur and purple-faced langur. Besides them, forest is also home for the other primates in Sri Lanka, such as toque macaque and red slender loris and other herbivorous mammals, such as Asian elephants (Elephas maximus), spotted deer (Axis axis), sambar (Rusa unicolor), and wild boar (Sus scrofa). The area is also home to a full complement of potential predators such as black eagles (Ictinaetus malaiensis), crested serpent eagles (Spilornis cheela), brahminy kites (Haliastur indus), white-bellied sea eagles (Haliaeetus leucogaster), leopards (Panthera pardus), fishing cats (Prionailurus viverrinus) and Indian rock pythons (Python molurus).

Endemic snakes such as Sri Lanka flying snake, Boiga barnesii, Dendrelaphis bifrenalis, Dendrelaphis oliveri, Oligodon sublineatus are frequently seen. Venomous snakes like Indian cobra, Russell's viper and Hypnale hypnale. Numerous types of skinks and lizards are also found.