In the Hawaiian Archipelago, shelter-dependent juvenile stages of many reef fishes and their coral habitats are increasingly put at risk by multiple anthropogenic stressors (e.g. overfishing and habitat loss, coral bleaching and sedimentation, respectively). We assessed coral bleaching (to identify relative susceptibility among growth forms) and the use v. availability of structurally complex and simple corals by juvenile reef fishes in Hawai'i. We use these data in a model that identifies habitats and resource species for managing reef fisheries and conserving coral habitats. Many juvenile reef fishes preferentially inhabit rugose corals. The economic and ecological importance of these fishes varies from those with little value to others, such as highly prized parrotfishes that also serve as ecological engineers. Coral species also differ in their relative susceptibility to anthropogenic and natural stressors – more structurally complex corals tend to be more susceptible to stressors. Our model relates the economic and ecological valuations of fish resources with specific preferences of fish juveniles for corals of varying susceptibility, testing the prediction that risk should co-vary among species of corals and fishes. Managers should use such a model when prioritising habitats and resource species for conservation.