Trajectories of decline in coral reefs have been attributed to the synergistic effects of changes in atmospheric pCO2 driving increases in seawater temperature and ocean acidification and human induced disturbances across the globe. For decades, coral bleaching has been autonomously aligned with the decline in coral health and is expected to increase in frequency over the coming decades due to increases in seawater temperature. However, much variation exists around when and how a coral bleaches and the associated costs sustained by the coral holobiont in regards to recovery and mortality risk. As bleaching is typically linked to thermal stress, considerable effort in the past has been invested into identifying upper thermal thresholds in corals and has focused on coral bleaching as a proxy for these. However, coral bleaching has not always been shown to result in mortality, as the links are poorly defined, and thus sheds uncertainty over the relationship between a bleaching threshold and an upper thermal limit. The objective of this thesis is to determine the dynamics and accuracy of identified thermal thresholds in two reef-building corals on the Great Barrier Reef across short term (daily) and seasonal time scales in response to variations in heat accumulation. This thesis uses measures of photosynthetic activity (Fv/Fm, P/R ratios, net Pmax), pigments (xanthophyll pool and cycling), symbiont densities and biochemical composition (host proteins, total lipid stores) to determine changes to Acropora formosa and Acropora millepora collected from an offshore (Heron Island, GBR) and inshore reef (Orpheus Island, GBR) during exposure to experimental treatments. Key findings include: (1) reductions in Fv/Fm (the quantum yield of PSII often linked to photosynthetic activity and coral bleaching) does not always coincide with a reduction in symbiont cells, photosynthetic activity and lipids/proteins; (2) Minor differences in heating rate (0.5 and 1ºC) can have distinct effects on both coral and symbiotic photosynthetic productivity, symbiont density and biochemical composition over the duration and recovery of a heating event; (3) Early summer thermal anomalies do not alter the temperature associated with the onset of bleaching or its severity (defined as % symbionts lost) in response to late summer anomalies, however, marginal differences in symbiont photosynthesis suggests some physiological “memory” in endosymbiotic dinoflagellates to early season thermal stress; and (4) P to R ratios < 1 in winter months suggests a reliance on heterotrophy for growth, reliance on previously deposited fat or a slow decline through the winter season in A. Formosa, which may have ramifications on the stress response. Finally, this thesis investigates the applicability of employing an in situ time x temperature model for determining bleaching thresholds (adapted from Berkelmans 2002) for use in developing GBR wide, but region specific, bleaching thresholds using satellite derived SST data. It was concluded that due to the variations in the success of the method, that this model may best serve as a monitoring tool that aims to detect and follow changes to predicted thresholds over time. In combination with the physiological observations of this thesis, this tool will assist in understanding the variations in the thermal stress response of corals and help better assess the future trajectories of corals under a changing climate.