Seagrass habitats support some of the most productive marine communities and provide critical habitat for many fish species. Previous studies have shown that fish communities of seagrass meadows are usually more diverse than those of adjacent habitats. However, most studies have been conducted in very shallow waters and generally have used seining methods to collect fish, which tend to select for slower species as well as small species and size classes. Antillean–Z style fish traps were used to study the fish communities of seagrass and associated habitats in both deep and shallow waters of Shark Bay, Western Australia. While more individuals were caught per trap in vegetated than in unvegetated habitats, the number of species and biomass was influenced by an interaction of depth and seagrass cover. The structure of fish communities was influenced by an interaction among season, seagrass cover, and depth. Unlike previous studies, a small number of species dominated fish trap catches, most notably, striped trumpeters, Pelates sexlineatus Quoy and Gaimard, 1925 and western butterfish, Pentapodus vitta Quoy and Gaimard, 1824. The factors that influenced the abundance of common species, including season, depth, and seagrass cover, often interacted and varied among species. This study suggests that future research on fish communities of seagrass ecosystems would benefit from using several sampling techniques and considering multiple environmental factors simultaneously.