Tropical seagrass meadows are critical habitats for many fish species, yet few studies have investigated the influence of multiple scale-dependent factors and marine protected areas on seagrass fish species of differing life histories. We assessed the influence of fine-scale seagrass meadow characteristics and seascape-scale variables on the abundance of fish in a seagrass-dominated seascape in the Bazaruto Archipelago, Mozambique, particularly examining patterns of nursery- vs. resident species as well as mobile- vs. sedentary species. We found that fish distribution patterns in this seagrass-dominated seascape were dependent on species’ life history characteristics; nursery taxa showed lower abundance in seagrass meadows further from adult reef habitats, while resident species within seagrass meadows occurred in higher abundances far from reefs. For taxa utilizing both mangroves and seagrass meadows as nursery habitat, proximity to mangroves was an important factor. Fish abundances were generally influenced by variables at the seascape scale (km), while sedentary species were predominantly influenced by area variables, and smaller seascapes (<500 m in radius) better explained distribution patterns. The influence of marine protected areas was taxon-specific, with the strongest effects of protection on resident species. Our results indicate that protection efforts in seagrass-dominated seascapes can have varying impacts on fish distribution, depending on the life history of the species present, and the geographical placement of the reserve within the seascape. Further, we suggest that simple species attributes can be utilised to describe generalized abundance patterns of fish in seagrass seascapes.