The spatial variability in the food chain structure of an estuarine environment(Nanakita estuarine, Japan) was investigated using stable carbon and nitrogen isotope. Potential organic matter sources(TP:Terrstrial Plant, MPOM:Marine particulate organic matter, BMA:Benthic microalgae, EPOM:Estuarine particulate organic matter), sedimentary organic matter and benthic invertebrates(Nuttallia olivacea and Nereidae) were sampled at four locations with different tidal flat types(e.g. sanddy, sanddy-muddy and muddy). The main objective of the present study was to determine food sources of Nuttallia olivacea and Nereidae along with small-scale spatial variability within the community of benthic invertebrates. TP(${delta}^{13}C=-26.6{pm}0.76$ and ${delta}^{15}N=2.7{pm}0.31$) and EPOM(${delta}^{13}C=-25.5{pm}0.13$ and ${delta}^{15}N=5.2{pm}0.46$) were isotopically distinct from BMA(${delta}^{13}C=-16.3$ and ${delta}^{15}N=6.2$) and MPOM(${delta}^{13}C=-19.6{pm}0.08$ and ${delta}^{15}N=8.9{pm}1.70$). ${delta}^{13}C$ values of sedimentary organic matter showed a distinct gradient in the range of -27.4 to -22.8‰ with a declining trend from the upstream to the downstream stations. The stable carbon and nitrogen isotope values of benthic invertebrates in the study site was -22.8 to -18.4‰ for ${delta}^{16}C$ and 8.1 to 11.9‰ or ${delta}^{15}N$, respectively. Mixing model(Isosource) calculations based on stable isotope measurements showed that benthic invertebrates of Nuttallia olivacea and Nereidae were found to be dominated by MPOM and BMA in stations. Whereas, TP and EPOM showed little influence to benthic invertebrates. The current result suggests that the different contribution for benthic invertebrates should be affected by both seasonal variation and physical factor among stations.