Thermal coral bleaching events (CBEs) over the Pacific, including those over the Great Barrier Reef (GBR), have commonly been linked to the El Niño–Southern Oscillation (ENSO), with bleaching reported to be a direct result of sea surface temperature (SST) anomalies driven by El Niño. However, such a relationship cannot explain CBEs that occurred during La Niña or the neutral phase of the ENSO. Here we show that the GBR is characterized by a significant negative correlation between total cloud cover anomaly (TCCA) and lagged SST anomaly (SSTA) whose magnitude and spatial extent are greater than the SSTA-ENSO correlation. This significant negative TCCA-SSTA (lagged) correlation prevails over two-thirds of the study domain even after the ENSO signal is removed, which suggests that local-scale reduced cloud cover is a key component of the regional warm shallow water formation over the GBR and the occurrence of thermal CBEs.