Two decades of coral monitoring reveal thermal stress thresholds on Indonesian reefs

Climate change threatens coral reefs, with a global decline in coral cover driven primarily by rising sea surface temperatures (SST) that cause mass bleaching and mortality. However, long-term trends in hard coral cover on Indonesian reefs, the epicentre of global coral diversity and home to ~10% of the world's reef area, remain largely unquantified. Here, we examined the relationship between long-term coral cover trajectories and thermal stress across 394 reef sites in 32 locations throughout Indonesia, using monitoring data collected between 2004 and 2023, with individual sites surveyed for three to sixteen years. We used generalized additive mixed-effect models (GAMMs) to quantify how the extreme thermal events of 2010 and 2016 affected coral cover. Over the past four decades, SSTs have increased by 0.12–0.28 °C per decade, with pronounced warming in eastern Indonesia. Despite these increases, long-term coral cover remained stable at the majority of study locations (26 out of 32), potentially due to high thermal tolerance and rapid recovery in some regions. Our analysis also revealed a significant negative relationship between the thermal stress metric Degree Heating Weeks (DHW, °C-weeks) and changes in coral cover, with substantial declines observed only beyond a critical threshold of >12 DHW. This study underscores the need for a comprehensive, coordinated national strategy to monitor coral cover and bleaching responses to thermal stress. Given the increasing frequency and intensity of marine heatwaves since 2016, especially in eastern Indonesia, such monitoring is essential to inform targeted strategies that support the resilience of Indonesian coral reefs.