The aim of this study was to create detailed geomorphic zonation and dominant benthic cover type maps of the shallow offshore reefs in the Cairns to Cooktown management area of the Great Barrier Reef. Maps such as these do not exist for the Great Barrier Reef, but would provide an invaluable resource for management agencies.The maps display the geomorphic zonation and dominant benthic cover type. Membership rules for object classification were based on OBIA rules, geomorphic zonation and expert knowledge/field data. It is important to note that the imagery used for the mapping process had a resolution of 15 m x 15 m, which would likely not capture the spatial variability of the benthic categories mapped.This dataset consists of shapefiles and auxiliary files for each of the geomorphic zonation and dominant benthic cover types on the shallow offshore reefs of the Cairns to Cooktown Management area of the Great Barrier Reef, Australia.