Several key species of the reefs of CINP have global populations that are already depleted, and the effects of fishing anywhere in the world affect the sustainability of these species. Tens of millions of sharks and rays are killed each year due to targeted fishing, as a result of by-catch in fisheries targeting other species or discarded as unwanted bycatch.

These are long-term climate changes that may be related to global warming and other climate events outside the natural range of variation that can lead to the disappearance of a species or habitat. They cause bleaching and loss of corals, vertical migration of reef species in search of cooler waters, substitution of coverage, or imbalances that threaten the health of the ecosystem.

It affects the penetration of light and therefore lowers water productivity in the bottom as it covers algae and corals and inhibits growth.

This comes from wastewater, soapy water, hydrocarbons, and others that are usually associated with the behavior of visitors and island officials. Additionally, plastic waste, mostly caused by ghost fishing, affects the ecosystems of Cocos Island National Park and its surrounding waters. Often, fishing equipment gets broken or lost and ends up entangled in a reef of CINP, causing damage to the resident species of the reef.

These are introduced species (terrestrial mammals and flora) that, among other consequences, increase soil erosion and sedimentation in the reefs. In some cases they compete with local fauna and could cause alterations in population structure that affect a whole chain. There are currently 5 species of introduced mammals in CINP (white-tailed deer, wild pig, domestic cat, black rat, and European rat) and at least 100 introduced plant species.