Many fish populations have experienced declines in recent decades due to anthropogenic disturbances, such as overfishing and habitat exploitation. Despite management actions, many populations show a limited capacity to recover. This may be attributed to reversal of predator-prey roles, yet empirical evidence to that effect remains scarce. Here, we combine field and laboratory studies to investigate the interaction between pike (Esox lucius), a large keystone top predatory fish, and the small-bodied mesopredatory threespine stickleback (Gasterosteus aculeatus) in the Baltic Sea where pike populations have declined. Our data suggest that stickleback predation on pike larvae depletes a large proportion of the recruitment and influences the size distribution through size-selective predation, which is corroborated by a gape-limitation experiment and diet analysis of wild-captured sticklebacks. The effects of stickleback predation are present across several populations and years, and our data suggest that early arrival of sticklebacks has stronger effects on juvenile pike survival. Finally, we use data on pike gape-limitation and the size distribution of sticklebacks to illustrate the process of role reversal. These findings suggest that mesopredator behaviour can reduce recruitment of a top predator species and impair the capacity of populations to recover. This emphasizes predator-prey role reversal as an important ecological and evolutionary driver that influences the outcome of restoration and management actions.