The coral reef crisis has exacerbated the need for improved understanding of coral demography at large scales. In particular, the population structure, spatial distribution and abundance of different corals across a range of distinct habitats will inform projected trends in coral cover and composition. Close-range photogrammetry provides unprecedented opportunity to document the size and location of individual coral colonies across a range of habitats, depths and spatial scales. This study utilises photogrammetry to create large-area orthomosaics and 3D models to explore the size structure and spatial distribution of two different coral taxa across three reefs, four sites around each reef, and two depths at each site, on Australia’s Great Barrier Reef. Our results will provide insights into the implications of differences in size structures and spatial patterns in coral population viability. The role of colony size, location and spacing on coral vital rates is particularly relevant to increase and monitor restoration success as well as to inform the where and how of restoration interventions.