Local meteorology over the Great Barrier Reef (GBR) can significantly influence ocean temperatures, which in turn impacts coral ecosystems. While El Niño–Southern Oscillation (ENSO) provides insight into the expected synoptic states, it lacks details of the anticipated sub-seasonal weather variability at local scales. This study explores the influence of the Madden-Julian oscillation (MJO) on Australian tropical climate, both independently and in combination with ENSO, with a focus on impacts to the GBR. We find that during El Niño periods, a faster propagating MJO pattern can disrupt background warm, dry conditions, and potentially provide cooling relief via increased cloud cover and stronger winds. Conversely, in La Niña periods, the MJO is prevented from passing the Maritime continent, forcing it to remain in a standing pattern in the Indian Ocean. This leads to reduced atmospheric convection over the GBR, decreased cloud cover and wind, and the generation of a warm ocean anomaly.