Sustained and widespread degradation of coral reef ecosystems is threatening the viability of coral populations and communities. Changes in percent cover is largely used to assess population viability, however variations in the size-frequency distribution of coral colonies would provide more nuanced ecological data especially at large spatial scales and/or for large sampling sizes. Here, we examined the size structure of six dominant coral morpho-taxa at three offshore and two inshore reefs of the central region of the Great Barrier Reef. We explored the variation in size structure among depths, sites and reefs, as well as between years. Our results suggested an overall increase in colony size between 2021 and 2022 for all morpho-taxa and highlighted differences in the size structure with marked variation among locations. We found that while some taxa showed constrained size structure with minor variations between habitats, other taxa such as tabular Acropora exhibited strong patterns suggesting that environmental factors such as wave exposure are likely modifying the size structure. Unveiling the relationships between environmental conditions and demographic rates of key coral taxa is particularly relevant to inform the where and how of restoration interventions.