The landforms in the park are associated with rocky mountains (of marble and limestone) running from north to south that forms spectacular limestone formations.

Two-thirds of the area is covered by lush tropical rainforest from the shoreline to the highest peak, and one third is thinly vegetated karst limestone. The vegetation types include lowland forest (often with a 35 m canopy), coastal forest and karst forest.

Mitrephora lanotan, Calamus ornatus var. philippinensis, Shorea polysperma, Diospyros pulgarensis, Dimorphocalyx luzoniensis, Beilschmiedia cairocan, Cryptocarya palawanensis, Ficus balete, Schizostachyum diffusum, Amomum palawanense, Dracontomelon dao, Pometia pinnata

Acerodon leucotis, Amblonyx cinereus, Mydaus marchei, Arctictis binturong, Hylopetes nigripes, Sundasciurus rabori and Hystrix pumila.

The PPSRNP is currently a popular destination for visiting bird-watchers, and most of the threatened and restricted-range birds of the Palawan Endemic Bird Area have been recorded there: Egretta eulophotes, Polyplectron, Chloropsis palawanensis emphanum, Tringa guttifer, Cacatua haematuropygia, Prioniturus platenae, Otus fuliginosus, Collocalia palawanensis, Anthracoceros marchei, Ixos palawanensis, Copsychus niger, Malacocincla cinereiceps, Malacopteron palawanense, Ptilocichla falcata, Ficedula platenae, Cyornis lemprieri, Terpsiphone cyanescens, Parus amabilis, Prionochilus plateni

Socio-economic

Small areas adjacent to the park had been cleared for cultivation in the early 1990s, which could pose a serious long-term threat to the forests inside the park. Some logging has recently been reported from inside the park, and the gathering of rattans would pose a major problem if left unchecked.

Puerto Princesa Subterranean River National Park (PPSRNP) was declared by Proc. No. 835 on 26 March 1971. Expanded to 22,202 has under Proc. No. 212 and inscripted as a World Heritage Site.

Palawan and associated islands are included in a Biosphere reserve, declared in 1990. An integrated management plan has been prepared for the whole Palawan Biosphere Reserve (ECAN), to zone the island, incorporate the existing PPSRNP and other protected areas which includes terrestrial core zone (primitive wilderness area are strictly protected) and buffer zone (regulated use allowed) areas. 

Protected. The park is relatively well-manned and actively managed by the local government of Palawan.

Directory of Philippine Wetlands Vol I & II, PBCPP, Key Conservation Sites in the Philippines, Philippine National Reports on Wetlands