Humans disproportionately target predators due to their higher economic and social value. This has led to widespread declines of predators in ecosystems worldwide leading to far-reaching effects on ecosystem processes. We investigate how the loss of predators from nearshore ecosystems due to fishing affects individual prey behaviour using a gradient of protection as a natural experiment. We collected data on piscivorous predator assemblages, reef habitats and prey behaviour within and outside two marine protected areas (MPAs) in the South Andaman Islands, India. As expected, predator abundance was significantly greater within MPAs. Similarly, we found greater coral cover and reduced algal cover within MPAs. In response, prey species, which included herbivorous and invertivorous fish, exhibited reduced movement and heightened vigilance inside MPAs. Additionally, prey individuals foraged at higher rates within MPAs. Habitat complexity and resource availability had complex effects on prey behaviours that varied across guilds. Our findings suggest that fishing directly alters the seascape of fear through the removal of predators. Fishing may also shape prey behaviour and ecological interactions indirectly through habitat degradation. Overall, this study highlights the need to study both direct and indirect consequences of human interactions with wild animals to understand their combined impacts on ecosystems. Keywords: