Tidal wetlands are important blue carbon reservoirs, but it is unclear how sea-level rise (SLR) may affect carbon cycling and soil microbial communities either by increased inundation frequency or via shifting plant species dominance. We used an in-situ marsh organ experiment to test how SLR-scenarios (0, + 7.5, + 15 cm) and vegetation treatments (Spartina alterniflora, Spartina patens, Phragmites australis, unvegetated controls) altered CO2 fluxes (net ecosystem exchange, ecosystem respiration), soil carbon mineralization rates, potential denitrification rates, and microbial community composition. Increasing inundation frequency with SLR treatments decreased the carbon sink strength and promoted carbon emissions with + 15-cm SLR. However, SLR treatments did not alter soil chemistry, microbial process rates, or bacterial community structure. In contrast, our vegetation treatments affected all carbon flux measurements; S. alterniflora and S. patens had greater CO2 uptake and ecosystem respiration compared to P. australis. Soils associated with Spartina spp. had higher carbon mineralization rates than P. australis or unvegetated controls. Soil bacterial assemblages differed among vegetation treatments but shifted more dramatically over the three-month experiment. As marshes flood more frequently with projected SLR, marsh vegetation composition is predicted to shift towards more flood-tolerant S. alterniflora, which may lead to increased CO2 uptake, though tidal marsh carbon sink strength will likely be offset by increased abundance of unvegetated tidal flats and open water. Our findings suggest that plant species play a central role in ecosystem carbon dynamics in vegetated tidal marshes undergoing rapid SLR.