Effective management of threatened and endangered species requires an understanding of how species of conservation concern are distributed spatially, as well as the spatial distribution of risks to the population, such as predation or human impacts (fishing, pollution, and loss of habitat). Identifying high-risk areas is particularly important when designing reserves or protected areas. Our novel approach incorporates data on distribution, movement, and diet of a generalist marine predator (harbor seals) to identify and map “hot spots” of predation risk for an endangered prey species (rockfish). Areas with high concentrations of seals (including some current marine reserves) are also estimated hot spots for rockfish predation. Although marine reserve planning currently targets areas with good habitat and low human disturbance, our modeling suggests that future terrestrial and marine reserve design may be made more effective by incorporating other components of the food web that either directly or indirectly interact with target species.