Whether through sea level rise or wetland restoration, agricultural soils in coastal areas will be inundated at increasing rates, renewing connections to sensitive surface waters and raising critical questions about environmental trade-offs. Wetland restoration is often implemented in agricultural catchments to improve water quality through nutrient removal. Yet flooding of soils can also increase production of the greenhouse gases nitrous oxide and methane, representing a potential environmental trade-off. Our study aimed to quantify and compare greenhouse gas emissions from unmanaged and restored forested wetlands, as well as actively managed agricultural fields within the North Carolina coastal plain, USA. In sampling conducted once every two months over a two-year comparative study, we found that soil carbon dioxide flux (range: 8000–64 800 kg CO2·ha−1·yr−1) comprised 66–100% of total greenhouse gas emissions from all sites and that methane emissions (range: −6.87 to 197 kg CH4·ha−1·yr−1) were highest from permanently inundated sites, while nitrous oxide fluxes (range: −1.07 to 139 kg N2O·ha−1·yr−1) were highest in sites with lower water tables. Contrary to predictions, greenhouse gas fluxes (as CO2 equivalents) from the restored wetland were lower than from either agricultural fields or unmanaged forested wetlands. In these acidic coastal freshwater ecosystems, the conversion of agricultural fields to flooded young forested wetlands did not result in increases in greenhouse gas emissions.