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Indonesia is home to the world's largest and most biodiverse coral reef system, spanning more than 32,000 square kilometres across the archipelago. Just like what is happening globally, these reefs are now bearing the brunt of a warming ocean.
Our new study, however, found that despite rising sea temperatures, coral cover at most of our Indonesian study sites remained remarkably stable over the long term.
Our study compiled long-term coral monitoring data from across Indonesia. Spanning from 2004 to 2023, the dataset covers 394 permanent reef sites across 32 locations. This massive effort was made possible primarily through data shared by the National Research and Innovation Agency (BRIN), Yayasan Konservasi Alam Nusantara, the Wildlife Conservation Society Indonesia Program, WWF Indonesia and Operation Wallacea.
Out of the 32 locations, 26 showed no significant overall change in hard coral cover, two actually saw an increase and four experienced a decline. Crucially, this stability persisted even as sea surface temperatures rose significantly across every single study location between 1985 and 2023, with the fastest warming occurring in eastern Indonesia.
While this is undoubtedly good news, it comes with a major warning: stability does not mean safety. Once heat stress becomes too frequent or too severe, coral loss can accelerate rapidly.
Much of the stability we observed is based on how reefs responded to earlier major heat events, especially those in 2010 and 2016.
Although these past events triggered bleaching and coral loss in several regions, they may not fully capture the unprecedented heat stress that reefs are now beginning to face.
Our findings, however, should not be interpreted as evidence that Indonesian reefs are safe from climate change. While many reefs have weathered past heat stress, increasingly frequent and intense warming could push these vital ecosystems past the point of recovery.
Marine heatwaves are becoming increasingly frequent and intense worldwide. The National Oceanic and Atmospheric Administration (NOAA) confirmed the fourth global coral bleaching event, reporting that bleaching-level heat stress had impacted roughly 84.4% of the world's coral reefs between January 2023 and September 2025.
Indonesia is no exception to this global trend, with bleaching incidents linked to the 2023-2025 marine heatwave documented across multiple locations, including reefs north of Jakarta, Karimunjawa in Central Java, and Raja Ampat's Dampier Strait.
Read more: Why coral reefs damaged by blast fishing struggle to recover - even after decades
When we compared changes in coral cover with accumulated thermal stress, we found that coral cover remained stable under low-to-moderate heat but dropped sharply once that stress crossed a critical threshold of around 12 degree-heating weeks (DHW).
DHW is a metric that combines both how much hotter the water is than usual and how long that heat persists. Think of it as a cumulative "heat dose" for coral reefs. For instance, 12 DHW could mean 12 weeks of water temperatures sitting 1C above the usual summer maximum - or six weeks at 2C above it.
In our study, coral loss became significantly more likely once temperatures surpassed 12 DHW. In other words, many Indonesian reefs appear capable of absorbing moderate heat stress - but only up to a point.
It is worth noting that "stable" here refers to total live hard coral cover, the only metric consistently tracked across Indonesia's various monitoring programmes. However, coral cover alone does not tell the whole story. A reef can maintain stable overall cover even as it loses many branching corals or large, old coral colonies, becomes dominated by just a few resilient species, or suffers a loss in structural complexity.
Indonesia's reefs do not all respond to heat stress in the same way. While some coral communities can recover quickly after bleaching, others struggle - particularly where pollution, sedimentation, destructive fishing and coastal development sap their capacity to bounce back.
Our study highlights that even reefs within marine protected areas (MPAs) cannot escape bleaching when ocean temperatures soar. Protected status cannot stop the ocean from warming, but it can significantly improve recovery prospects by alleviating local pressures.
In Aceh, reefs around Weh Island were ransacked by the 2010 bleaching event. Remarkably, some managed to rebound to pre-bleaching levels of coral cover within roughly six years, a recovery likely aided by long-term protection.
In contrast, in Lombok, particularly around Sekotong Bay, recurrent and intense heat stress has triggered substantial coral loss, including a major decline following the severe 2016 bleaching event. Compounding the problem, these reefs have also been battered by multiple localised human pressures, which have likely impeded their ability to bounce back.
These examples illustrate why climate change and local reef management cannot be treated in isolation. While reducing localised pressures will not prevent bleaching during extreme heatwaves, it can give reefs a much-needed fighting chance to survive and recover in their wake.
Our study is the first national-scale analysis to link long-term changes in coral cover in Indonesia with thermal stress across such a large number of monitored reefs.
Without long-term monitoring, we cannot tell which reefs are coping with heat stress, recovering after bleaching or slowly declining.
If Indonesia is to protect its reefs effectively, it needs a stronger and more coordinated national strategy for monitoring coral condition and bleaching impacts. This framework must look beyond mere coral cover to track bleaching severity, mortality rates, recovery trajectories, juvenile recruitment, community composition and structural changes over time.
As the ocean continues to warm, the future of Indonesia's reefs will depend not only on their natural tolerance but also on our ability to safeguard the very conditions that allow them to heal.
