The Great Barrier Reef (GBR) World Heritage Area and adjacent Coral Sea Marine Park are under serious threat from global climate change. This study used Daily Optimally Interpolated Sea Surface Temperature (DOISST) data to identify major marine heatwaves (MHWs) that have occurred in this region over the last three decades (1992–2022). We then used Himawari-8 (H-8) SST data to map significant MHW events that occurred between 2015 and 2022. We investigated the mechanisms underlying the MHWs, assessed thier impact on shallow and mesophotic coral reef ecosystems and identified potential coral refugia. MHWs in this region have increased in frequency, intensity and spatial extent. El Niño, especially when it is in phase with positive Indian Ocean Dipole, was the key remote driver leading to intense MHWs. However, the more recent strong MHWs (e.g., 2017 and 2022) occurred in the abscence of these climatic events, signifying the impacts of long-term climate change and local drivers. We also found that reduced wind speed and shoaling mixed layer depth, often together with reduced cloudiness, were the main local drivers pre-conditioning these MHWs. Anomalous air-sea heat flux into the ocean, mainly controlled by shortwave solar radiation (cloudiness) and latent heat flux (wind), was the most constant contributor to the 2015–16 and 2019–20 MHW events. However, local oceanographic dynamics, especially horizontal advection and turbulent mixing, played important roles in MHW heat budgets. This study confirmed that shallow-water coral bleaching severity was positively related to the cumulative MHW intensity in the 2015–16 and 2019–20 MHW events. We identified shallow reefs along the path of the North Queensland Current as potential coral refugia from bleaching because of the cooler waters upwelled from the ocean current. We also found that, except during weather events such as tropical cyclones, mesophotic reefs in the Coral Sea Marine Park may be less susceptible to severe bleaching as the MHWs were more confined within the shallow mixed layer.