ABSTRACT: Previously we have demonstrated that prey availability to seabirds of the Great Barrier Reef (GBR) decreases in direct association with within-season increases in sea-surface temperature, independent of prevailing El Niño conditions. These negative impacts occur throughout the GBR and affect multiple seabird species. Currently, the oceanic processes driving these impacts or the potential for them to occur in other marine systems are unknown. Here, we use satellite and in situ data obtained during a thermal stress event to identify the within-season links between ocean dynamics and seabird foraging success on the southern GBR. In February 2006, a major mesoscale eddy formed coastward of the East Australian Current flow, adjacent to our study site. In mid-February, strengthening of this eddy caused an intrusion of cool, dense waters at depth across the GBR shelf. This intrusion intensified vertical stratification and caused a pronounced warming of sea-surface layers. Prey availability to seabirds significantly decreased during this period and remained low until eddy intensity decreased and surface waters cooled. Prey availability increased following this episode, clearly indicating that loss of prey was associated with a short-term vertical and/or horizontal redistribution of forage-fish, or subsurface predators, rather than an overall decrease in productivity linked to seasonal-scale El Niño processes.