In tropical seascapes, coral reefs often exist in proximity to marine vegetated habitats such as seagrass, mangroves, and macroalgae. This habitat mosaic offers the possibility for connection and exchange of both organisms and nutrition between habitats, mediated by biological and physical processes. This dissertation examines flows of organisms and nutrition between coral reefs and tropical vegetated habitats in the central Red Sea through 3 different mechanisms: 1) Use of multiple habitat types by tropical marine fishes, 2) Transport of algal material to coral reefs via the foraging behavior and movements of herbivorous fishes, and 3) Physical flow of water between coastal habitats. The results of this thesis suggest that coastal tropical habitats maintain a variety of ecological links at different spatial and temporal scales. A large fraction (36%) of fish species found on coral reefs are also found in at least one marine vegetated habitat in the central Red Sea, with many species mainly living in vegetated habitats as juveniles. This demonstrates the value of mangrove, seagrass, and macroalgae habitats to coral reef fishes, and suggests that many species make ontogenetic migrations between reef and non-reef habitats through their lives. Two species of herbivorous reef fishes (Naso elegans and N. unicornis) were found on coral reefs with algae in their guts which likely originated from nearby Sargassum-dominated macroalgae canopies, representing a fish-mediated, cross-habitat flux of nutrition from macroalgae habitats to coral reefs. Finally, we used a combination of remote sensing, a dye tracer study, and in-water measurements to observe water movement from shallow seagrass and mangrove habitats to nearby lagoon and coral reef habitats. Water exiting seagrass and mangrove habitats had altered concentrations of various nutrients (such as increased particulate organic carbon or decreased dissolved nutrients), suggesting that Red Sea mangroves and seagrasses change nutrient concentrations in water and the movement of water from these habitats to coral reefs could supply reefs with an allochthonous source of nutrition. These various linkages, controlled by a range of physical and biological processes, highlight the interconnected nature of tropical coastal ecosystems, and thereby the need to conserve whole habitat mosaics in the pursuit to protect coral reefs and maintain healthy and functioning coastal ecosystems.