The spatial variation of organic matter sources in tidal flat sediment of the Nanakita River estuary, involving Gamo lagoon on the north-east coast of Honshu Island, Japan, was examined using carbon stable isotopes and fatty acid biomarkers. The spatial variation of total organic carbon (TOC) contents and ${delta}^{13}C$ values were highly variable in between the stations, such as sandy flat (1.3 mg/g, -21.0‰), sand-muddy flat (2.6 mg/g, -21.9‰), and muddy flat (24.9 mg/g, -25.9‰), respectively. Particularly, at the muddy flat, high TOC content and low ${delta}^{13}C$ value of the sediments indicated that the surface sediment was composed largely of terrestrial organic matter. Whereas, at the sandy flat and sand-muddy flat, the high ratios of diatom and bacteria biomarkers indicated the high contribution of abundant microorganism along with marine organic matter in sediment composition. From these results, it considered that the amount and origin of transported sedimentary organic matter indicated different characteristics in this study stations.