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The coastal Gulf of Mexico (GOM) and Coastal Sea off Korea (CSK) both suffer from human-induced eutrophication. We used a N-mass balance model in two different regions with different nitrogen input sources to estimate organic carbon fluxes and predict future carbon fluxes under different model scenarios. The coastal GOM receives nitrogen predominantly from the Mississippi and Atchafalaya Rivers and atmospheric nitrogen deposition (AN-D) is only a minor component in this region. However, in the CSK, groundwater and atmospheric nitrogen deposition are more important controlling factors. Our model includes the fluxes of nitrogen to the ocean from the atmosphere, groundwater, and rivers, based on observational and literature data, and identifies three zones (brown, green and blue waters) in the coastal GOM and CSK with different productivity and carbon fluxes. Based on our model results, the potential primary production rate in the inner (brown water) zone are more than 2 (GOM) and 1.5 gC m−2 day−1 (CSK). In the middle (green water) zone, potential production is between 0.1 to 2 (GOM) and 0.3 to 1.5 gC m−2 day−1 (CSK). In the offshore (blue water) zone, productivity is less than 0.1 (GOM) and 0.3 (CSK) gC m−2 day−1. Through our model scenario results, overall oxygen demand in the GOM would increase approximately 21 % if we fail to reduce riverine N input, likely increasing considerably the area affected by hypoxia. Comparing the results from the U.S. with those from Korea shows the importance of considering both riverine and atmospheric inputs of nitrogen. This has direct implications for investigating how changes in energy technologies can lead to changes in the production of various atmospheric contaminants that affect air quality, climate and the health of local populations.