Abstract The Puerto Princesa Underground River, amongst the largest caves of the Philippine Islands, is the most visited show cave in the country, even though it has undergone no tourism adaptation at all. Its scientific importance primarily relies on the fact that it is one of the largest known underground estuaries in the world, and the effect of tides is visible along more than 7 km of the cave length. The complex relationships between sea and freshwater influence not only the hydrodynamics of the system and the speleogenetic processes presently active, but also its climate and its ecosystem. The systematic exploration and research of this coastal karst system started some 40 years ago and have shown that the Puerto Princesa Underground River is one of the most important caves in the world with regard to many different scientific fields. Speleogenesis concerns the initial phreatic solution followed by vadose erosion with periodical marine invasion, and subsequent saline/freshwater-mixing processes during sea-level highstands. The hydrodynamic behaviour of the water flowing inside the cave is rather complex, being simultaneously controlled by allogenic recharge and tides. Speleothems abundantly occur with several forms, some of which have never been described before. Several minerals, some of which are very rare, are present, together with palaeontological remains exposed by differential corrosion on rock walls. Last but not least, two large populations of bats and swiftlets sustain a complex subterranean ecosystem.