Community dynamics on coral reefs are often examined only in relatively shallow waters, which are most vulnerable to many disturbances. The Great Barrier Reef World Heritage Area (GBRWHA) includes extensive submerged reefs that do not approach sea level and are within depths that support many coral reef taxa that also occur in shallow water. However, the composition of benthic communities on submerged reefs in the GBRWHA is virtually unknown. We examined spatial patterns in benthic community composition on 13 submerged reefs in the central Great Barrier Reef (GBR) at depths of 10-30 m. We show that benthic communities on submerged reefs include similar species groups to those on neighbouring emergent reefs. The spatial distribution of species groups was well explained by depth and cross-shelf gradients that are well-known determinants of community composition on emergent reefs. Many equivalent species groups occurred at greater depths on submerged reefs, likely due to variability in the hydrodynamic environment among reef morphologies. Hard coral cover and species richness were lowest at the shallowest depth (6 m) on emergent reefs and were consistently higher on submerged reefs for any given depth. These results suggest that disturbances are less frequent on submerged reefs, but evidence that a severe tropical cyclone in 2011 caused significant damage to shallow regions of more exposed submerged reefs demonstrates that they are not immune. Our results confirm that submerged reefs in the central GBR support extensive and diverse coral assemblages that deserve greater attention in ecosystem assessments and management decisions.