Various species of aquatic animals have complex life cycles and utilize different habitats during consecutive phases of their life cycles. For example, many marine fish species occupy different habitat types during juvenile and adult life stages. Juveniles of some species recruit to inshore nursery habitats such as mangroves and seagrass beds, whereas large adults tend to dominate coral reefs. The mechanisms underlying apparent cross-habitat distribution patterns by life stage remain uncertain for many species. Here, we investigated potential mechanisms that produce a 5-phase, and possibly even a 6-phase life cycle pattern in a common Caribbean coral reef fish species Haemulon flavolineatum (French grunt) across multiple coastal habitats. At each discrete life stage, individuals were faced with important and stage-specific ecological trade-offs that could significantly augment fitness. Pelagic larvae settled on rubble habitats near bay entrances where they reached an optimum between predation risk (survival) and food abundance (growth). Individuals subsequently shifted to seagrass beds, likely as a result of increased food resources, followed by a shift to mangroves as predation refugia. Before the uni-directional movement between bays and coral reefs, some fishes shifted from mangroves to boulder/notch habitats. Likely, this habitat serves as an intermediate stop before their final shift to the coral reef, where they reach maturity and reproduce. This study reveals ecological linkages and flows among habitat types that are of direct conservation importance to these ecosystems. Furthermore, the identification of mechanisms that give rise to cross-habitat distribution patterns of marine fishes in general might lead to enhanced conservation management solutions to declines in fisheries at larger scales.