Surface sediment from the coastal bays of Gwangyang and Masan in South Korea were analyzed for their contents and isotopic values of organic carbon and total nitrogen. The sources and diagenetic alteration of organic matter were also assessed. Total organic carbon varied from 0.22% to 3.48% (average = 1.40%, n = 75), and C/N ratios varied from 2.4 to 15.2 (average = 8.79, n = 75). ${delta}^{13}C_{org}$ ranged from -19.92‰ to -25.86‰ (average = -21.21‰, n = 75), and ${delta}^{15}N_{TN}$ ranged from 8.57‰ to 3.93‰ (average = 6.49‰, n = 75). Total organic carbon in both areas was associated with grain-size, with higher contents in finer grained sediment. The high carbon content observed in Masan Bay sediment correlated with its higher C/N ratio. ${delta}^{13}C_{org}$ and ${delta}^{15}N_{TN}$ varied widely, attributable to various influences such as the input of terrestrial organic matter and diagenetic alteration. The depleted ${delta}^{13}C_{org}$ and higher ${delta}^{15}N_{TN}$ observed in the sediment of Gwangyang Bay reflected terrestrial supply, implying that biogeochemical processes, i.e. bacterial degradation, were more active in Masan Bay sediment, which showed less depleted ${delta}^{13}C_{org}$ and higher ${delta}^{15}N_{TN}$ than Gwangyang Bay sediment. ${delta}^{15}N_{TN}$ was the more useful indicator of biogeochemical processes in the highly anoxic sediment. These results indicate that the ${delta}^{13}C_{org}$ and ${delta}^{15}N_{TN}$ of sedimentary organic matter in coastal bays can indicate the source and degree of diagenetic alteration of sedimentary organic matter.