The positioning of habitats interacts with variability in abiotic factors (e.g. seasonal changes in temperature and extreme weather events) to change how animals use a land or seascape. Marine reserves can regulate how human activities alter fish communities and increase the abundance of targeted species, but the combined influence of reserves and seascape context on species habitat use remains uncertain in many ecosystems. Further, marine reserve effectiveness might be low for mobile species if the size of the reserve is less than a species usual range, reducing the overall time a individual may be protected. In this study, we tracked 19 giant shovelnose rays (Glaucostegus typus), an IUCN listed vulnerable species within the Moreton Bay Marine Park in eastern Australia. We used an array of 28 acoustic receivers within a complex mosaic of seagrass patches, bare sand, mangrove forests and deep-water channels and used regression tree analyses to determine which spatial, temporal and protection factors contributed most to G. typus habitat use. Overall, 50% of the total detections in the study occurred inside marine reserves containing large seagrass beds (>7.09 m2) and in close proximity to mangroves (<7.47 km). During winter (<20.2 °C), G. typus centre of activity increased significantly (p < 0.001), and greater than 50% of the detections occurred in reserves in winter. Conversely, during the rest of the year (water temperature > 20.2 °C), the habitat use of individuals is contained in smaller centres of activity compared with winter, however, protection effects varied. Our results show that seascape context and marine reserves combine to provide the optimal areas for G. typus habitat selection. Limited food resources likely caused larger centres of activity during winter. Identifying priority habitats for vulnerable species is critical for ongoing protection and maintaining effective conservation initiatives. We have shown here that incorporating spatial features into the design of marine reserves can improve conservation outcomes for mobile benthic predators such as G. typus and other species that use such seascapes.