Here, we utilise a unique, 70-year-long (1949–2017), high-resolution historical aerial imagery dataset to track changes to coral reef structures in Bill’s Bay on the Ningaloo coast. Reef habitat was distinguished from sand and rubble substrates based on imagery greyscale values and autoclassified using unsupervised image analysis in ArcMap. This approach was validated through comparison of reef structure (defined by bathymetric LiDAR imagery), greyscale values of aerial photography taken during the same survey, and in-water ground-truthed photographs. Long-term (1990–2015) live coral cover data were then compared with changes in reef structure. Reef structure increased from 11 to 38% within Bill’s Bay between 1949 and 1990. A coral spawn-induced hypoxia event in 1989 caused a loss of live coral cover from 50 to 7%, a 25% reduction in reef structure by 2002, and a switch from branching to massive coral-dominated reef. From 2002, reef structure recovered and continued to expand, peaking at 41% of total area (2017). Live coral cover in 2015 (46%) matches this measured increase in reef structure, despite a drop in coral cover in 2008. Discrepancies observed between live coral cover and reef structure during the 2002–2010 period reflect the persistence of the massive dominated coral community and in situ dead reef framework. Across the entire study period, reef growth was most prominent along the south-western edge of the bay, possibly due to an increase in the availability of hard substrate for coral recruitment. This study provides new insights into reef health over decadal timescales by capturing changes in reef geomorphology that go beyond the spatial scale and scope of traditional in-water assessments. These data further highlight that coral reef structure in Bill’s Bay has expanded even with frequent natural disturbances affecting the region over the last 70 years.