Mediterranean rocky reefs are undergoing regime shifts, from a structurally complex and diverse state dominated by canopy- forming macroalgae to a degraded one characterised by low-lying turf or encrusting macroalgal species, due to increased anthropogenic pressure and climate change. Using data gathered from 89 sites across the entire Aegean Sea, this study aims to provide the most comprehensive health status assessment of shallow rocky reefs in the area, based on macroalgal community structure. Overall, 2520 benthic images were collected through photoquadrat sampling at 0, 5 and, 15 m depth. Five macroalgal and seven invertebrate morphofunctional groups, along with four substrate categories, were considered for community structure description. Health status was assessed using the reef-EBQI and EEI-c indices. Results indicate turf as the most widespread macroalgal group (36.8% average area cover), followed by encrusting calcareous (16.6%), shrubby (12.7%), articulated calcareous (8.9%), and canopy-forming algae (3.7%). Bare rock also occupied a substantial surface area (9.0%) with highest cover (13.8%) at 5 m. The area cover of canopy-forming algae was particularly low, ranging from 10% at 0 m to 0.1% at 15 m depth, on average. All depths pooled, according to the reef-EBQI index, the ecological status of the Aegean Sea was estimated to be ‘Bad’, mainly due to the bad ecological status of the 5 and 15 m stations. At 0 m depth, the status of the Aegean Sea was ranked ‘Moderate’ according to the reef-EBQI index and ‘Good’ according to the EEI-c index. The results underline the importance of considering a wide depth range when assessing the health status of rocky reef communities.