The Great Australian Bight is a large carbonate cold water environment located on the central and western portions of the southern Australia. Seagrasses (Posidonia sp.) and macroalgae benthic habitats are widely distributed in the shallow water environment of southern Australia, contributing to the carbonate factory. This study investigated the distribution of modern benthic foraminiferal assemblages in the microtidal wave-dominated inner-shelf of Esperance Bay (southwestern Australia), that lies on the western margin of the Great Australian Bight. Benthic foraminifera were taxonomically identified and biotic parameters (species richness, density, Fisher-α index, Shannon-Weaver index, dominance) were calculated. Multivariate analyses (Hierarchical Cluster Analysis, Principal Component Analysis) were performed to understand foraminiferal distribution in the context of environmental conditions. Four main foraminiferal assemblages have been recognized: (I) a nearshore assemblage of dense seagrass meadow, dominated by Lamellodiscorbis dimidiatus, Elphidium craticulatum, Elphidium crispum, Cibicides lobatulus, II) a second assemblage associated with unvegetated seabed (approximately 30 m depth) with Lamellodiscorbis dimidiatus, Elphidium crispum, Quinqueloculina disparilis, III) a third assemblage in the central sector of the bay, characterized by a discontinuous and mixed seagrass-algae coverage with Lamellodiscorbis dimidiatus, Elphidium crispum, Elphidium macellum, Cibicides refulgens, and Quinqueloculina poeyana, and IV) an epiphytic assemblage of transitional zone from the coastline to the upper limit of a mixed seagrass-algae meadow, dominated by Elphidium crispum, Chrysalidinella dimorpha, Planulinoides biconcava, Planoglabratella opercularis, Rugobolivinella elegans. The spatial distribution of the four assemblages appears closely related to sediment texture, seagrass cover and depth, but it is also influenced by the shoreface morphology and the hydrodynamic energy. The understanding of the ecological parameters that influence benthic foraminiferal distribution, composition and assemblage structure within seagrass meadows is useful for paleoecological and paleoenvironmental interpretations.