Coral reefs were damaged by an exponential increase in fishing over an approximately 20,000-hectare (77 sq mi) area around the TWNC.

[5] Its marine conservation has attracted individual visitors and national and international institutions such as UNESCO,[3] the IUCN, the World Bank, Phantera,[6] and UNODC.

[9][failed verification] The mantangan plant (Meremia peltata), a flowering vine in the morning glory family which limits trees' access to sunlight, is an environmental challenge.

Several areas in TWNC have eroded as much as 20 metres (66 ft) due to rising sea levels triggered by global warming.

[10] Although it is the third country classified as a "lung of the world", Indonesia faces a challenge in sustaining funding for its conservation activities.