The Great Barrier Reef (GBR) is of immense biological, cultural and economic importance, but has also rapidly degraded over the last 30 years. Improved spatial information on reef geomorphic zonation and benthic cover type (including coral type) is critical to support scientific work to understand how the GBR is changing, and to support resource management decisions that enable conservation of the reef and its essential ecosystem services. Yet, no comprehensive maps exist that detail the geomorphic zonation or benthic cover for the GBR’s ~ 3000 reefs. This study presents three new types of shallow reef maps for 237 reefs in the central Cairns Management Region of the GBR Marine Park (GBRMP), explores how the detailed habitat maps created compared to current maps and posits how the new maps may support and refine current critical key science outputs and management challenges. Geomorphic Zonation, Benthic Cover and Coral Type habitat maps were created using a unique combined object-based image analysis and ecological modelling approach that incorporated satellite imagery, limited field data and key reef physical attributes (depth, slope, waves) using a previously peer-reviewed mapping approach developed for the Capricorn Bunker Group reefs, Southern GBR. The mapping approach was consistent and repeatable, suggesting applicability to mapping all 3000 reefs in the GBRMP. Compared to existing maps that only outline each reef, the increase in detail provided by these new habitat maps enabled discrete characterisation of each reef’s geomorphology and benthic composition. With the new habitat maps, areas within each reef can be identified as either coral habitat or not coral habitat. This has not been possible previously. As such, a model of coral ecological and biophysical processes that depends on bottom reflectance of sand and coral areas can be fine-tuned. Similarly, for reef restoration, nursery structures are commonly placed in non-coral habitats, and/or coral larvae are dispersed in areas of known coral habitat. The new habitat maps presented permit more accurate identification of these areas such that restoration projects can be targeted more effectively. These findings confirm the need to now apply this mapping approach to the full extent of the GBR.