The accumulative impact of the intensive scallop culture on the bottom environment and polychaete community structure were studied in Saroma Lagoon, northern Japan. The bottom sampling was carried out in 1995, and the multivariate analysis have been used to compare 1975, 1987 data with 1995 data. 55 species were identified in 1995 samples, among them the dominant species were Maldane cristata, Lumbrineris longifolia and Scalibregma inflatum, which were typical species in Japanese eutrophic coastal bays. The result of comparative analysis of the polychaete community structure during period of the past 20 years showed marked changes in species number, density and species composition. The species composition of polychaete community in 1995 indicates that the lagoon environment may not be in the state of heavily organic pollution. But clear temporal changes in the community structure and frequent occurrence of spreading hypoxic water and red tides in recent time suggest the accumulative organic loading by the intensive scallop culture in the lagoon may cause severe bottom hypoxia, eutrophication of water and stressful disturbances to the benthic community.