Quantifying the ecological importance of individual habitats to highly mobile animals is challenging because patterns of habitat reliance for these taxa are complex and difficult to observe. We investigated the importance of lagoons to the manta ray, Manta alfredi, a wide-ranging and vulnerable species in a less-disturbed atoll ecosystem. Lagoons are highly sensitive to anthropogenic disturbance and are known to be ecologically important to a wide variety of mobile species. We used a novel combination of research tools to examine the reliance of M. alfredi on lagoon habitats. Stable isotope analysis was used to assay the recent energetic importance of lagoons to M. alfredi; high-resolution tracking data provided information about how M. alfredi utilised lagoonal habitats over long and short time periods; acoustic cameras logged patterns of animal entrances and departures from lagoons; and photo identification/laser photogrammetry provided some insight into why they may be using this habitat. M. alfredi showed strong evidence of energetic dependence on lagoon resources during the course of the study and spent long periods of residence within lagoons or frequently transited into them from elsewhere. While within lagoons, they demonstrated affinities for particular structural features within this habitat and showed evidence of temporal patterning in habitat utilization. This work sheds light on how and why M. alfredi uses lagoons and raises questions about how this use may be altered in disturbed settings. More generally, these observations contribute to our knowledge of how to assess the ecological importance of particular habitats situated within the broader home range of mobile consumers. © 2014 Springer-Verlag Berlin Heidelberg.