The capacity of reef-building corals to adapt to global warming depends upon standing heritable variation in tolerance traits upon which selection can act. While heat tolerance is known to differ markedly among coral taxa and reefs, limited knowledge exists on within-species variation among spatial scales ranging from meters to hundreds of kilometers. Here, we performed standardized acute heat stress assays to quantify the thermal tolerance of 768 colonies of Acropora spathulata from 14 reefs spanning 1060 km (9.5° latitude) of the Great Barrier Reef (GBR). Colony thermal tolerance was determined by the rate of decline in physiological traits under +3 °C, +6 °C and +9 °C above the local maximum monthly mean (MMM). Photochemical efficiency and chlorophyll retention traits revealed considerable variation in thermal thresholds among individual colonies both among reefs (~6 °C) and within reefs (~3 °C). Although tolerance rankings of colonies varied between traits, the most heat tolerant corals (i.e. within the top 25% of each trait) were found at virtually all reefs across the GBR, indicating widespread phenotypic variation. Reef-scale environmental predictors explained 12–62% of trait variation and heat tolerance was the greatest at reefs exposed to high thermal averages and recent thermal stress likely reflecting local adaptation and stress pre-acclimatization. We also found evidence that heat tolerance was further influenced by thermal fluctuations, ocean currents and cloud cover. Importantly, heat tolerance relative to local summer temperatures was the greatest in the southern GBR (~9.5 °C above MMM), suggestive of higher potential to adapt to future warming. Together, these results can be used to identify naturally tolerant coral populations and individuals for conservation and restoration applications.