Bundala harbors various forms of fishes including salt water dispersants Anguilla bicolor, marine forms Ambassis gymnocephalus, brackish water forms Chanos chanos and freshwater forms Channa striata. Bundala's herpetofauna includes two endemic species, a toad and a snake, Bufo atukoralei and Xenochrophis asperrimus. Among reptiles are Mugger crocodile Crocodylus palustris, Estuarine crocodile Crocodylus porosus, Common Monitor Varanus bengalensis, Star Tortoise Geochelone elegans, Python Python molurus, rat snake Pytas mucosus, endemic flying snake Chrysopelea taprobana, cat snakes Boiga spp. and whip snakes Dryophis spp. The adjacent seashore of Bundala is a breeding ground for all five species of globally endangered sea turtles that migrate to Sri Lanka.
The ecological areas of the national park contain seven terrestrial habitat types and six wetland types. The dry thorny shrubs and herbs being the most abundant plant life. A total of 383 plant species belonging to 90 families have been recorded from the park"The Phytoplankton in all the lagoons is dominated by blue-green algae" including species such as Macrocystis, Nostoc, Oscillatoria.[ Hydrilla is in abundance in lagoons such as Embilikala and Malala. Water hyacinth, water lilies, and Typha angustifolia reed beds are found in the marshes and streams. The vegetation mainly consists of Acacia scrubs including Dichrostachys cinerea, Randia dumetorum, Ziziphus sp., Gymnosporia emarginata, Carissa spinarum, Capparis zeylanica and Cassia spp. The trees of the forest are Bauhinia racemosa, Salvadora persica, Drypetes sepiaria, Manilkara hexandra, and less common Chloroxylon swietenia, Azadirachta indica, and Feronia limonia. Halophyte plants thrive in the national park's environmental conditions. Salicornia brachiata and Halosarcia indica are examples of salt-tolerant plants. In the small degraded patch of mangrove found at the Bundala lagoon area, Lumnitzera racemosa trees are widespread.
The Bundala National Park has been identified as an outstanding Important Bird Area in the South Indian and Sri Lankan wetlands.324 species of vertebrates have been recorded in the national park,which include 32 species of fish, 15 species of amphibians, 48 species of reptiles, 197 species of birds and 32 species of mammals. 52 species of butterflies are among the invertebrates.The wetland habitats in Bundala harbours about 100 species of water birds, half of them being migrant birds. Of 197 avifaunal species 58 are migratory species. National Bird Ringing Programme (NBRP) was launched in Bundala by in collaboration of Department of Wildlife Conservation and Field Ornithology Group of Sri Lanka in 2005
Black-necked Stork Ephippiorhynchus asiaticus, Lesser Adjutant Leptoptilos javanicus and Eurasian Coot Fulica atra are rare birds inhabit in the national park.
A few Elephant Elephas maximus still inhabits in the forests of Bundala. Other mammals seen in the park are Toque Macaque Macaca sinica, Common Langur Presbytis entellus, Jackal Canis aureus, Leopard Panthera pardus, Fishing Cat Felis viverrinus, Rusty-spotted Cat Felis rubiginosa, Mongoose Herpestes spp., Wild boar Sus scrofa, Mouse Deer Tragulus meminna, Indian Muntjac Muntiacus muntjak, Spotted Deer Cervus axis, Sambar C. Unicolor, Black-naped Hare Lepus nigricollis, Indian Pangolin Manis crassicaudata, and Porcupine Hystrix indica.
