The microhabitats and the composition of living benthic foraminiferal faunas in the sediments deposited off the Rhône River mouth are directly influenced by the Rhône River input. In this shallow-water environment (20–98 m water depth), the vertical distribution of the species is not well defined, probably due to the low penetration of oxygen into the sediment. We show the existence of two types of species: “predominantly superficial” taxa showing a density maximum in the topmost sediment layer, and “potentially/ predominantly infaunal taxa” that are also frequent in the topmost sediment, but which show considerable densities in anoxic deeper sediment layers as well. In the area that is strongly influenced by river input (near the river mouth and in the southwestern direction, following the river plume), the fauna is composed mostly of “potentially/predominantly infaunal” species adapted to a higher contribution of terrestrial organic matter, generally of lower quality, and to the low penetration of oxygen into the sediment. This fauna is composed of species tolerant to strong environmental stress (e.g., Nonionella turgida, Nonion scaphum, Rectuvigerina phlegeri, and Valvulineria bradyana). The stations less influenced by fluvial input (located south and east of the river mouth) are composed of species that colonize oxygenated interstices in the upper centimeter of sediment. The dominant species are mainly “predominantly superficial” taxa (e.g., Cassidulina carinata, Bulimina aculeata), which are known to react quickly to provisions of labile organic matter. The correlation between these two types of faunas and the two prevalent environmental factors suggests that the vertical distribution of living foraminifera in front of the Rhône River mouth is primarily controlled by the quality of the organic matter and less by the quantity of the organic matter and depth of oxygen penetration into the sediment.