This study documented surface distributions of live and dead foraminiferal assemblages in the low-gradient tidal marshes of the barrier island and estuarine complex of the eastern Mississippi Sound (Grand Bay, Pascagoula River, Fowl River, Dauphin Island). A total of 71,833 specimens representing 38 species were identified from a gradient of different elevation zones across the study area. We identified five live assemblages and nine biofacies for the dead assemblages from estuarine, low marsh, middle marsh, high marsh, and upland transition environments. Although dissolution of calcareous tests was observed in the dead assemblages, characteristic species and abundance patterns dependent on elevation in the intertidal zone were similar between living assemblages and dead biofacies. The assemblages from the eastern Mississippi Sound estuaries were dominated by Ammonia tepida, Cribroelphidium poeyanum, C. excavatum, and Paratrochammina simplissima. The low marshes were dominated by Ammotium salsum, Ammobaculites exiguus, and Miliammina fusca. The dominant species in the middle marshes was Arenoparrella mexicana. The most abundant species in the high marshes was Entzia macrescens. The upland–marsh transition zones were dominated by Trochamminita irregularis and Pseudothurammina limnetis. Canonical correspondence analysis was applied to assess the relationship between a priori defined biofacies and measured environmental data (elevation, grain size, organic matter, and salinity) to test the hypothesis that distribution of foraminiferal assemblages is driven by elevation and hence flooding frequency. Salinity was the second most important explanatory variable of dead assemblages. Riverine freshwater from the Pascagoula River markedly influenced the live and dead assemblages in the Pascagoula River marsh, which was represented by low diversity and densities and dominance by Ammoastuta inepta. The relationship between the measured environmental variables and assemblage distributions can be used in future Mississippi Sound paleo-environmental studies.