The Dampier Archipelago in north west Australia, has high marine diversity and one of Australia’s busiest ports. In offshore waters adjacent to the archipelago is an important suite of demersal fisheries. The study aimed to build on the limited knowledge of the endemic blue spotted emperor, Lethrinus punctulatus, a short-lived, commercially important fish species in the region. To achieve this, the present study examines the distribution of L. punctulatus across a continuous depth gradient and its association with a variety of habitat and environmental variables using baited remote underwater stereo-video systems (stereo-BRUVs). Stereo-BRUVs were deployed across a continuous depth gradient, and a variety of substrata and habitat types, from inside the Dampier Archipelago and out into the offshore waters to 50 m depth and ~100 km offshore. Different size classes of L. punctulatus, showed strong associations with particular depths, shifting from shallow to deep water as they became larger, such that while abundance was fairly uniform across depths, biomass increased with increasing depth. In shallow coastal waters, juveniles of this species were found to be disassociated with complex reef habitat, where predatory fish maybe abundant, and instead were positively associated with macroalgal habitat. Our quantitative study validates historical fisheries legislation that acted to protect shallow water habitats, that were thought to be important to juvenile life stages of commercially important fish species in the Pilbara region.