The Coral Sea Marine Park (CSMP) is the largest marine reserve in Australian waters, covering 989,836 km2 off the eastern coast of Queensland. The closest reef within the CSMP to the Australian mainland coast is 200 km away, while the furthest reef is more than 1000 km away. The combination of size and distance from the mainland have led to this marine park being understudied when compared to its marine reserve neighbour, the Great Barrier Reef Marine Park. Our team conducted a reef lagoon benthic habitat mapping project for the CSMP in December 2022. Our survey included five different reef systems – Lihou Reef, Tregrosse Reef, Herald Cays, Holmes Reef, and Flinders Reef – an area of approximately 2,700 km2 in 11 days. We mapped benthic habitats to 80 meters in depth using rapid visual assessment techniques (underwater drop camera with video analysis). We found four deepwater seagrass meadows at three different reef systems, comprised of two seagrass species (Halophila ovalis and Halophila decipiens), and many large algal beds of mixed species (including extensive Halimeda bioherms). Our findings will assist Parks Australia in the management of this marine resource, by filling in knowledge gaps within Australia’s largest marine park.