Sea snakes are an important component of bycatch in commercial and small-scale trawl fisheries in tropical waters and are highly vulnerable to fishing-related mortality. Extensive boat-based surveys were conducted to investigate the assemblage and abundance of sea snakes within a protected shallow coastal bay adjacent to productive trawl fishing grounds. Spine-Bellied Sea Snakes, Hydrophis curtus (previously Lapemis curtus), and Elegant Sea Snakes, Hydrophis elegans, were the most commonly encountered species. Based on the age structure of these two species, the bay was used primarily by juveniles. Temporal trends in age structure and sex ratios showed that H. curtus may use Cleveland Bay as a nursery ground, with gravid females entering the bay in summer months to give birth. In contrast, H. elegans appears to use the bay more consistently through the year, with ∼30% of individuals being adults. This study also showed that shallow tidal habitats, too shallow for trawl fishing, are regularly used by sea snakes and may provide refugia for vulnerable life stages. The identification and protection of such habitats may further mitigate risks to sea snake populations from trawl fishing.