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The importance of mangrove and seagrass lagoonal habitats as nursery areas for many reef-associated fish species is well established in the scientific literature. However, few studies have examined the relative use by nursery species of different sub-habitats within such systems. Here, we investigated fish community structure of a variety of interconnected sub-habitats of the tropical lagoon of Lac Bay in Bonaire, Dutch Caribbean. Visual census was used to test the degree to which these sub-habitats may differ in their use by fishes of different species and life stages. We quantitatively sampled the fish species abundance, composition, and size structures at a total of 162 sites distributed among nine different sub-habitats that are common to mangrove and seagrass ecosystems. Fish community variables differed consistently among sub-habitats and were mainly influenced by the presence of mangrove root structure or seagrass cover. Mangrove fringe sub-habitats were a premier habitat since multiple life stages of a variety of species showed highest densities and biomass there. Several reef fish species had a distribution pattern suggesting a unique stepwise post-settlement life cycle migration in which larger juveniles and/or subadults appear to move from the open bay environment (seagrass beds or bay mangrove fringe) to the interior mangrove fringes along mangrove pools before later departing to the adult habitat of the coral reef. In the case of the well-lit and well-circulated central bay sub-habitat, the limiting factor to fish abundance and diversity appeared to be the paucity of three-dimensional shelter due to the lack of Thalassia seagrass beds. In the warm and hypersaline backwaters, physiological tolerance limits were likely a key limiting factor. Long-term changes driven by mangrove expansion into this non-estuarine lagoon have been steadily reducing the net coverage of clear bay waters, while the surface of shallow, muddy, and hypersaline backwaters, unusable by key nursery reef fish species, has been increasing by an almost equal amount. Our study shows how fish density varies along the full gradient of sub-habitats found across a tropical bay to provide insight into the potential consequences for nursery habitat function when the availability and quality of these sub-habitats change in response to the long-term dynamic processes of mangrove land reclamation and climate change.