The Temporal variability in the food chain structure of bacteria in the sedimentary organic matter was investigated using stable isotope and fatty acid. Potential organic matter sources (Land plant, Marine POM, benthic microalgae, Riverine POM), sedimentary organic matter and bacteria were sampled in Gamo largoon and Nanakita estuary. The main objective of the present study was to determine food sources of bacteria along with temporal variability. Land plant (${delta}^{13}C$ = -26.6‰ and ${delta}^{15}N$ = 3.6‰) and Riverine POM (${delta}^{13}C$ = -25.5‰ and ${delta}^{15}N$ = 8.9‰) were isotopically distinct from benthic microalgae (${delta}^{13}C$ = -16.3‰ and ${delta}^{15}N$ = 6.2‰) and Marine POM (${delta}^{13}C$ = -20.3‰ and ${delta}^{15}N$ = 10.3‰). ${delta}^{13}C$ values of sedimentary organic matter showed a distinct gradient in the range of -20.7‰ to -191‰. The stable carbon and nitrogen isotope values of bacteria in the study were -20.8‰ to -18.6‰ for ${delta}^{13}C$ and 6.5‰ to 8.6‰ for ${delta}^{15}N$. From this results based on stable isotope measurements showed that in the bacteria was found to be dominated by Marine POM and Benthicmicoralge during 0 to 20 day. Whereas, terrestrial plant and riverine POM showed little in fluence to bacteria during the experiment.