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Net ecosystem carbon balance is a comprehensive assessment of ecosystem function that can test restoration effectiveness. Coastal peatlands are globally important carbon sinks that are vulnerable to carbon loss with saltwater intrusion. It is uncertain how wetland carbon stocks and fluxes change during freshwater restoration following exposure to saltwater and elevated nutrients. We restored freshwater to sawgrass (Cladium jamaicense) peat monoliths from freshwater marshes of the Everglades (Florida, U.S.A.) that had previously been exposed to elevated salinity (approximately9 ppt) and phosphorus (P) loading (1 g P m⁻²year⁻¹) in wetland mesocosms. We quantified changes in water and soil physicochemistry, plant and soil carbon and nutrient standing stocks, and net ecosystem productivity during restoration. Added freshwater immediately reduced porewater salinity from >8 to approximately 2 ppt, but elevated porewater dissolved organic carbon persisted. Above‐ and belowground biomass, leaf P concentrations, and instantaneous rates of gross ecosystem productivity (GEP) and ecosystem respiration (ER) remained elevated from prior added P. Modeled monthly GEP and ER were higher in marshes with saltwater and P legacies, resulting in negative net ecosystem productivities that were up to 12× lower than controls. Leaf litter breakdown rates and litter P concentrations were 2× higher in marshes with legacies of added saltwater and P. Legacies of saltwater and P on carbon loss persisted despite freshwater restoration, but recovery was greatest for freshwater marshes exposed to saltwater alone. Our results suggest that restoration in nutrient‐limited freshwater wetlands exposed to saltwater intrusion and nutrient enrichment is a slow process.