Coastal wetlands are known for exceptional productivity, but they also receive intense land-based nitrogen (N) loading. In Narragansett Bay, RI (USA), coastal ecosystems have received anthropogenic N inputs from wastewater for more than two centuries. Greenhouse gas fluxes were studied throughout a growing season (2016) in three coastal wetlands with contrasting histories of nitrogen loading. The wetland with the highest historic N load (Mary’s Creek, Warwick, RI) had significantly greater nitrous oxide (N₂O) and methane (CH₄) emissions than the other two sites. However, the two marshes with historic N loads (Mary’s Creek and Mary Donovan, Little Compton, RI) also had greater rates of CO₂ uptake than the reference site (Nag Marsh, Prudence Island, RI). Their CO₂ uptake rates far outpaced their other greenhouse gas emissions. Mary’s Creek had the greatest above- and below-ground plant biomass, vertical accretion rates, and carbon content of soils. Spartina alterniflora height was greatest at Mary’s Creek and Mary Donovan marsh. The following growing season (2017), greenhouse gases were compared across four plant-defined ecological zones in Mary’s Creek. Higher rates of CO₂ uptake and CH₄ emissions were found in the S. alterniflora-vegetated creekbank compared to high marsh zones or bare mudflats. Potential denitrifying enzyme activity did not significantly differ across the four zones nor between Mary’s Creek and Nag Marsh, suggesting a consistently high capacity to completely reduce N loads. These results support efforts to protect and restore these coastal ecosystems for their carbon sequestration function even despite prevalence of anthropogenic N loading.