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Shallow reefs are a major feature of coral assemblages in the Andaman Sea. At Phuket, Thailand sheltered reefs are dominated by massive corals, together with an increasing abundance of branching species during favourable growth conditions. The growth of coral on these reefs is moderated by long‐term increases in sea temperature and relative sea level but fluctuating decadal/intradecadal climate processes of El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD), which modulate sea level and temperature, are the main drivers of coral cover. In this study, the contribution of these two climate processes was identified and also quantified. Over a 34‐year study of fluctuating coral cover, the three major reductions in cover in 1997, 2010 and 2019 were linked to overlapping positive IOD (pIOD) and El Niños in 1997 and 2019, and with an El Niño alone in 2010. Combined pIOD and El Niño depressed sea level was the major factor in reducing cover in 1997 while El Niño extreme sea temperatures were responsible for large reductions in 2010. In 2019, a bi‐phasic pIOD and El Niño resulted in lowered cover at a time of both decreased sea level and high sea temperature. Under global warming scenarios, it is projected that extreme pIODs, such as those seen in 1997 and 2019, will occur more frequently while El Niño frequencies will continue to increase even after global mean temperature stabilization. In these circumstances, and with steadily rising background sea temperatures, the future risks to the shallow reefs of the Andaman Sea are substantial, despite any temporary respite gained from climate related or land subsidence sea‐level rise. Such findings have wider implications for all reefs affected by climatic‐driven sea‐level depressions, particularly those around Indonesian shores where similar El‐Niño‐related reductions in coral cover have been reported.