Salt marshes have among the highest carbon (C) burial rates of any ecosystem and often rely on C accumulation to gain elevation and persist in locations with accelerating sea level rise. Net ecosystem carbon balance (NECB), the accumulation or loss of C resulting from vertical CO 2 and CH 4 gas fluxes, lateral C fluxes, and sediment C inputs, varies across salt marshes; thus, extrapolation of NECB to an entire marsh is challenging. Anthropogenic nitrogen (N) inputs to salt marshes impact NECB by influencing each component of NECB, but differences in the impacts of fertilization between edge and interior marsh must be considered when scaling up. NECB was estimated for the 0.5 km 2 Spartina alterniflora marsh area of Freeman Creek, NC, under control and fertilized conditions at both interior and edge berm sites. Annual CO 2 fluxes were nearly balanced at control sites, but fertilization significantly increased net CO 2 emissions at edge sites. Lateral C export, modeled using respiration rates, represented a significant C loss that increased with fertilization in both edge and interior marsh. Sediment C input was a significant C source in the interior, nearly doubling with fertilization, but represented a small source on the edge. When extrapolating C exchanges to the entire marsh, including edge which comprised 17% of the marsh area, the marsh displayed net loss of C despite a net C gain in the interior. Fertilization increased net C loss fivefold. Extrapolation of NECB to whole marshes requires inclusion of C fluxes for both edge and interior marsh. Plain Language Summary Salt marsh ecosystems rely on carbon accumulation to increase elevation and survive sea level rise. The amount of carbon accumulated in a marsh is the net result of carbon dioxide emissions to the atmosphere, fixation of carbon by photosynthesis, export of dissolved carbon to the creek, and accumulation of organic carbon in sediments deposited on the surface. Because each component varies between edge and interior marsh, it is challenging to estimate carbon accumulation for a whole marsh system. It is not currently known how increasing nitrogen pollution impacts carbon accumulation for a whole marsh. To find out, we compared measurements of carbon accumulation in fertilized and unfertilized plots in the edge and interior of a salt marsh at Freeman Creek, North Carolina, USA. Overall, the marsh gained carbon in the interior but lost carbon on the edge, leading to a loss of about 50,000 kg C year −1 across the 0.5 km 2 marsh area. However, under fertilized conditions, Freeman Creek marsh carbon loss increased nearly fivefold overall as a result of the large increase in carbon loss from the edge marsh. This study shows that increasing nitrogen pollution in coastal waters will cause increasing net carbon loss in marshes.