Eelgrass (Zostera marina) loss occurs worldwide due to increasing water temperatures and decreasing water quality. In the U.S., widgeongrass (Ruppia maritima), a more heat-tolerant seagrass species, is replacing eelgrass in certain areas. Seagrasses enhance sediment denitrification, which helps to mitigate excess nitrogen in coastal systems. Widgeongrass and eelgrass have different characteristics, which may affect sediment nitrogen cycling. We compared net N2 fluxes from vegetated areas (eelgrass and widgeongrass beds, using intact cores that included sediment and plants) and adjacent unvegetated areas from the York River, in the lower Chesapeake Bay during the spring and summer of one year. We found that seagrass biomass, sediment organic matter, and NH4+ fluxes were significantly higher in eelgrass beds than in widgeongrass beds. Eelgrass was also net denitrifying during both seasons, while widgeongrass was only net denitrifying in the summer. Despite differences in the spring, the seagrass beds had a similar rate of N2 production in the summer and both had higher denitrification rates than unvegetated sediments. Both species are important ecosystem components that can help to mitigate eutrophication in coastal areas. However, as the relative composition of these species continues to change, differences in sediment nitrogen cycling may affect regional denitrification capacity.