Oysters are important marine foundation species across the world, particularly in estuaries of the Gulf of Mexico. One important function of oysters in estuaries is the provision of 3-dimensional habitat that is used by a wide range of species. In this study, the biotic diversity of mid-bay intertidal oyster reefs found in a Gulf of Mexico estuary was examined at nested ecological and demographic scales. Fishery-independent data collections made in East Matagorda Bay, Texas, USA, were used to compare community structure and diversity at mid-bay reefs to undifferentiated shoreline habitats. Despite similar diversity metrics, there were differences in community structure that were driven by differences in spatial habitat use by several common species. Below the community scale, demographic differences in spotted seatrout Cynoscion nebulosus habitat use were observed, with smaller and younger individuals found along reefs, and larger and older individuals found along shorelines. This finding was more pronounced for male spotted seatrout in the spring. The observed spatial habitat use patterns at nested ecological scales (community, inter-species, intra-species) highlight the importance of oyster reefs for maintaining diversity in Gulf of Mexico estuaries, and more broadly support the notion that heterogeneity in localized habitats drives biotic diversity at the estuary scale. Conservation of oyster reefs as critical habitat should be considered along with conservation of oysters themselves when balancing the ecological value of oysters against the commercial value of oyster fisheries.