Understanding variations in habitat use through time contributes to identification of habitats critical for species survival. Here we used passive acoustic telemetry to examine the residency and site fidelity patterns of the reef manta ray Mobula alfredi at Lady Elliot Island (LEI), a key aggregation site in eastern Australia. Six acoustic receivers were moored around LEI between 2009 and 2012, and 34 acoustic transmitters were deployed on manta rays. All tagged animals returned to this site within their recording period, with some individuals visiting the area for up to 23 consecutive days. Using a set of mixed effect models, we analysed the hourly visitation patterns of manta rays in relation to temporal and environmental variables. Diel phase and sea temperature showed the strongest effects on the presence of manta rays, with weaker effects detected for wind direction, wind speed and moon illumination. Individuals occupied LEI habitat mostly during daylight hours and in calm weather conditions, which may be linked with behavioural thermoregulation, social interactions and cleaning activities. Their absence at night may be related to foraging strategies in deeper offshore waters. The effect of sea temperature reflects the greater seasonal occurrence of manta rays at LEI in winter, when temperatures are coolest, potentially in response to regional food availability. The high degree of manta ray site fidelity at aggregation sites underscores the importance of these areas as key daytime habitats for the species. We suggest that conservation measures should prioritise the protection of coastal aggregation habitats from overexploitation and degradation.