Vessel traffic represents one of the most pervasive and escalating sources of disturbance in marine environments, affecting organisms through noise, physical presence, habitat degradation, collisions, and pollution. For some marine megafauna, including species of cetaceans, sirenians, fishes, pinnipeds, and marine reptiles, many of which are at high risk of extinction, effects of vessels are especially pronounced, well-documented, and recognized as a significant threat. Characterizing the potential effects of interactions between vessels and marine megafauna is necessary for effective science-informed management strategies. However, to-date these effects have not been comprehensively synthesized across species and ecosystems. To fill this gap, we conducted a global meta-analysis on the effects of vessels on marine megafauna, quantifying vessel effects on behavior, physiology, metabolism, and populations. Analysis of 1850 comparisons (‘vessel treatment and control scenarios’) across 204 peer-reviewed publications on 57 different species revealed that vessel effects vary widely across taxa and response types. Our systematic analysis provides a foundation for the development and implementation of multi-pronged management strategies to mitigate vessel-related threats to marine animals and enhance resilience in an era of increasing anthropogenic pressures.