Two types of deposit-feeding polychaetes, Neanthes japonica and Notomastus sp., and their surrounding sediments were collected from the Nanakita River Estuary and a small brackish lagoon (Gamo Lagoon) in northeastern Japan. The samples were examined using stable isotope analysis to assess the site specific feeding mode of the animals and their trophic status. N. japonica is a surface deposit-feeder and Notomastus sp. is a subsurface deposit-feeder. In the estuary, the sedimentary δ 5N tended to become isotopically heavier from the upper estuary (2.0 ∼ 3.9‰) to the river mouth (4.3 ∼ 6.2‰), while sedimentary organic δ 13C constant value (−26.8 ∼ −24.4, average −25.6‰) throughout the river estuary. The δ 13C values of N. japonica were similar to those of the surrounding sediment in the upper estuary, whereas in the lower estuary, N. japonica had a heavier δ 13C value than the surrounding sediment. The δ 13C and dg 15N values indicated that the carbon, but not the nitrogen, of N. japonica was derived from upland plants in the upper estuary. In the lower estuary, a significant fraction of carbon of N. japonica was derived from phytoplankton. Notomastus sp. exhibited heavier δ 13C values than the surrounding surface sediment throughout the estuary and had heavier δ 13C values than N. japonica in the same location. These results suggest selective utilization of sedimentary carbon by those animals following bacterial processing and subsequent fractionation. The difference in δ 15N between sedimentary organics and corresponding polychaetes was 5 ± 1‰ and rather higher than 3.4 ± 1.1‰ expected for normal trophic effects in other animals.