Coral reef fishes often exhibit specific or restricted depth distributions, but the factors (biotic or abiotic) that influence patterns of depth use are largely unknown. Given inherent biological gradients with depth (i.e. light, nutrients, habitat, temperature), it is expected that fishes may exploit certain depths within their environment to seek out more favourable conditions. This study used baited remote underwater video (BRUV) systems to document variation in the taxonomic and functional (trophic and size) structure of a fish assemblage along a shallow to upper-mesophotic depth gradient (13–71 m) at a submerged, offshore shoal in the northern Great Barrier Reef. BRUVs were deployed during two separate time periods (February and August 2017), to separately examine patterns of depth use. Both the relative abundance and diversity of reef fishes declined with depth, and there were pronounced differences in the taxonomic and functional structure of the fish assemblage across the depth gradient. In shallow habitats (< 30 m), the fish assemblage was dominated by herbivores, detritivores, planktivores and sessile invertivores, whereas the fish assemblage in deeper habitats (> 30 m) was dominated by piscivores and mobile invertivores. Depth and habitat type were also strong predictors for important fisheries species such as coral trout (Plectropomus spp.), emperors (Lethrinus spp.) and trevallies (Carangid spp.). We found limited evidence of temporal changes in depth and habitat use by fishes (including fisheries target species), although recorded temperatures were 4 °C higher in February 2017 compared to August 2017.