Hydrographers Passage lies on the continental margin of the central Great Barrier Reef (GBR) in northeastern Australia. The GBR margin represents the world's largest extant tropical siliciclastic/carbonate depositional system, which extends for about 2,300 km in length. This system is composed of shoreline, shelf, shelf edge and slope, and basin elements. The Hydrographers Passage site is currently the best-studied section of the GBR shelf edge and upper slope, comprising geomorphic features such as modern coral reefs, drowned or submerged reefs, a shelf platform draped with extensive dune fields, seaward terraces, and a smooth upper slope. Assessment of benthos at Hydrographers Passage utilized the still images obtained by the autonomous underwater vehicle (AUV) at two cross-shelf transects: in the northwest about 3.6 km long, from a deep reef across the terrace to the upper slope; and in the southeast about 2.7 km long, from a shallow reef across the platform and over a dune field. A method was developed to identify macrofauna trends based on the hypothesis that substrate is an important factor in the distribution of benthos. Sediment grabs from two cross-shelf transects show a generally similar composition of poorly-sorted, muddy sand, and iron stained carbonate gravel. In contrast, dune sediments are well-sorted sand with no iron staining. Images from two AUV transects provide the data for a hierarchical clustering of substrate types into five substrate groups: sand, gravel, rubble, sediment-covered limestone, and reef. The AUV imagery reveals a clear distinction between the benthos associated with hard substrate, and soft substrate habitats at a finer-scale than can be shown within the broader-scale geomorphic features. Maximum entropy modeling is used to generate a habitat preference map for azooxanthellate, filter-feeding octocorals.