Salt marshes are regarded as among the most productive coastal ecosystems, important “blue carbon” sinks and a support for benthic communities with large abundances, whose structure may be strongly influenced by salt marsh vegetation. During the last few decades, Spartina alterniflora has been colonizing bare mudflats in the Bahía Blanca estuary, and a large increase in the area covered by salt marshes has been reported. This colonization can strongly influence the structure of benthic fauna and its role in the carbon cycle. The hypothesis of this study was that the community structure and the organic carbon contained in the meio- and macrobenthos change between tidal flats and salt marshes recently colonized by S. alterniflora. Response variables studied to compare the tidal flat and salt marsh were density, biomass and production to biomass (P/B) ratio of macro- and meiobenthos. Density and biomass of Gastropoda and P/B ratio of Nematoda were higher on the salt marsh than on the tidal flat. By contrast, density and biomass of Polychaeta were higher on the tidal flat. These results suggest that the expansion of S. alterniflora marshes on tidal flats produces changes in the structure of the macro- and meiobenthos community (taxonomic composition and biomass) that have an influence on carbon cycling.