In the southern portion particularly in the Irawan area, metamorphic rocks of the Inagawan Formation can be found. The area is also partly composed of sedimentary Iwahig Formation, alluvium of unconsolidated gravel, sand, pebbles and silt. Some ultramafic rocks of the Palawan Ophiolite Complex also characterize the area.

The northern part of the City is comprised of ultramafic rocks. In particular, the Langogan area is characterized by metamorphic rocks consisting of quartz-feldspathic and mica schists, phyllites, slate and quartzites. The ultramafic rocks consist of unaltered sepertenized pridotite, dunite and pyrexomite.

Babuyan area is made up of Irahuan Metavolcanics which resemble the quartz-hematite schist in appearance and are also friable and weather into dark reddish gray platy fragments which are usually scattered near outcrops of river beds. St. Paul limestone outcrops as small patches are found in the south and midwestern part of the catchment. It is comprised of a very thick, massive, marbleized limestone with very well developed karst.

The Puerto Princesa Subterranean River National Park has  karsts limestone formation and is popular tourist destination among local and international tourists. The underground river is about 8.2 kilometers in length and has been proclaimed under Proclamation No. 212 as a National Park. The park covers a protected area of 22,202 hectares.  It is also included in the list of World Heritage Sites by UNESCO because of its diverse ecosystem and the presence of rare flora and fauna. The site, which is located in Sabang, barangay Cabayugan has also fine white beaches.