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 delta N-15 tended to become isotopically heavier from the upper estuary (2.0 similar to 3.9 parts per thousand) to the river mouth (4.3 similar to 6.2 parts per thousand), while sedimentary organic delta C-13 exhibited no such trend and maintained a rather constant value (-26.8 similar to -24.4, average -25.6 parts per thousand) throughout the river estuary. The delta C-13 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 delta C-13 value than the surrounding sediment. The delta C-13 and delta N-15 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 delta C-13 values than the surrounding surface sediment throughout the estuary and had heavier delta C-13 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 delta N-15 between sedimentary organics and corresponding polychaetes was 5 +/- 1 parts per thousand and rather higher than 3.4 +/- 1.1 parts per thousand expected for normal trophic effects in other animals.