ABSTRACT: Improving our knowledge on the behavior of threatened species is essential for developing effective conservation actions. The Paranaguá Estuarine Complex (PEC), southern Brazil, is the only estuary in the world where manta rays have been observed performing breaches seasonally. The exact role of this breaching behavior and the environmental factors connected to it are unknown. Our goals were to determine the spatial distribution, and the temporal and environmental factors that influence the breaching behavior of this endangered group in a dynamic estuarine habitat for the first time. Manta rays were observed breaching in the PEC during austral summer and early autumn, when the sea surface temperature (SST) and precipitation were high. Generalized additive models revealed that the presence and frequency of the breaches were both influenced by the SST and hours of daily effort, while the breaching frequency was also influenced by the wind direction and speed, percentage of moon illumination, and year. The breaches were mainly concentrated near the mouth of a river. Likely these factors influenced not only the occurrence and behavior of manta rays, but also the distribution of their food source, potentially providing optimal conditions for foraging and reproduction. Based on the coloration pattern, it is possible that the observations were of Mobula cf. birostris. These results provide valuable insights into the breaching behavior of manta rays in estuarine waters that will assist future conservation initiatives and research on their behavioral ecology, to optimize fishery management and contribute to developing sustainable ecotourism in the PEC.