Comparative physiology has developed a rich understanding of the physiological adaptations of organisms, from microbes to megafauna. Despite extreme differences in size and a diversity of habitats, general patterns are observed in their physiological adaptations. Yet, many organisms deviate from the general patterns, providing an opportunity to understand the importance of ecology in determining the evolution of unusual adaptations. Aquatic air-breathing vertebrates provide unique study systems in which the interplay between ecology, physiology and behavior is most evident. They must perform breath-hold dives to obtain food underwater, which imposes a physiological constraint on their foraging time as they must resurface to breathe. This separation of two critical resources has led researchers to investigate these organisms’ physiological adaptations and trade-offs. Addressing such questions on large marine animals is best done in the field, given the difficulty of replicating the environment of these animals in the lab. This Review examines the long history of research on diving physiology and behavior. We show how innovative technology and the careful selection of research animals have provided a holistic understanding of diving mammals’ physiology, behavior and ecology. We explore the role of the aerobic diving limit, body size, oxygen stores, prey distribution and metabolism. We then identify gaps in our knowledge and suggest areas for future research, pointing out how this research will help conserve these unique animals.