The legacy of multiple marine transgressions is preserved in a complex morphology of ridges, mounds and reefs on the Carnarvon continental shelf, Western Australia. High-resolution multibeam sonar mapping, underwater photography and sampling across a 280 km2 area seaward of the Ningaloo Coast World Heritage Area shows that these raised features provide hardground habitat for modern coral and sponge communities. Prominent among these features is a 20 m high and 15 km long shore-parallel ridge at 60 m water depth. This ridge preserves the largely unaltered form of a fringing reef and is interpreted as the predecessor to modern Ningaloo Reef. Landward of the drowned reef, the inner shelf is covered by hundreds of mounds (bommies) up to 5 m high and linear ridges up to 1.5 km long and 16 m high. The ridges are uniformly oriented to the north–northeast and several converge at their landward limit. On the basis of their shape and alignment, these ridges are interpreted as relict long-walled parabolic dunes. Their preservation is attributed to cementation of calcareous sands to form aeolianite, prior to the post-glacial marine transgression. Some dune ridges abut areas of reef that rise to sea level and are highly irregular in outline but maintain a broad shore-parallel trend. These are tentatively interpreted as Last Interglacial in age. The mid-shelf and outer shelf are mostly sediment covered with relatively low densities of epibenthic biota and have patches of low-profile ridges that may also be relict reef shorelines. An evolutionary model for the Carnarvon shelf is proposed that relates the formation of drowned fringing reefs and aeolian dunes to Late Quaternary eustatic sea level.