Context Coastal beach environments provide habitats for marine megafauna, including turtles, rays, marine mammals and sharks. However, accessing these variable energy zones has been difficult for researchers by using traditional methods. Aims This study used drone-based aerial surveys to assess spatio-temporal variation of marine megafauna across south-eastern Queensland, Australia. Methods Drones were operated at five south-eastern Queensland beaches. Megafauna sightings and key variables including location, month and turbidity were analysed to assess variation across locations. Key results Overall, 3815 individual megafauna were detected from 3273 flights. There were significant differences in the composition of megafauna assemblages throughout the year and among beaches, with megafaunal sightings in >80% of flights conducted off North Stradbroke Island. Conclusions Strong temporal presence was found that is congruent with other studies examining seasonality. This supports the use of drones to provide ecological data for many hard-to-study megafauna species and help inform long-term sustainable management of coastal ecosystems. Implications Results indicated that environmental conditions can influence the probability of sighting marine megafauna during aerial surveys.