Eutrophication and hypoxia are major problems affecting the health of coastal ecosystems throughout the world. Tokyo Bay, Japan, is a eutrophic coastal area where the abundance of the megabenthic community has been decreasing. To assess factors associated with the impaired biota, seasonal surveys of the megabenthic community and water and sediment quality were conducted in the bay. Cluster analysis showed a difference in the community structure between the northern and southern parts of the bay. The density of species and species diversity were high throughout the year in the southern part of the bay, whereas in the northern part of the bay species diversity was low and defaunation occurred in August. At this time, bottom hypoxia due to temperature and salinity stratification, and high concentrations of nutrients, chlorophyll a, and organic matter in the water column and/or sediment, dominated the northern part of the bay. In October, bottom hypoxia was less severe but was still present in the northern part of the bay, and recolonization by mobile fishes and sessile mussels occurred. Multivariate analyses of the megabenthic community and environmental parameters in August showed the spatial pattern of the community could be explained by concentrations of dissolved oxygen and particulate organic carbon in the bottom water, and total sulfide and total organic carbon in the sediments. In particular, impairment of the biota in the northern area could be explained by the threshold concentrations of dissolved oxygen < 1.7 mL L(-1) and total organic carbon > 20.3 mg g(-1).