Tokyo Bay consists of two parts: the outer part faces the Pacific Ocean and the inner part is semi-enclosed with limited water exchange. Hypoxia develops in the central to northern part of the bay and persists from spring to autumn. During summer, up to two-thirds of the bottom becomes hypoxic. After the hypoxic episode, when death and migration of the benthic fauna have occurred, the area is recolonized by the bottom fauna either through migration or larval settlement. Some species which have spawning peak in spring and summer may fail in reproduce due to hypoxia. Hypoxia may alter the sustainability of the Tokyo Bay ecosystem through changes in the spatial and temporal community structure of macrobenthic and mecabenthic organisms.

Bottom hypoxia in Tokyo Bay is caused by anthropogenic eutrophication. It is unclear when hypoxia began, some reports state anoxia already in 1929. In the first bottom water surveys it was observed in 1955, after which it has been increasing both spatially and in duration. In July 2004 hypoxia occupied 67% of the whole bay area.

Reclamation of land along the coast of the bay has been done since the end of the World War II. It has led to deterioration of water and sediment quality. After the war, human population and industrial activities increased in the metropolitan area surrounding the bay. Household wastewater from the surrounding urban areas heavily contribute to nitrogen and phosphorus inputs.

Nutrient inputs to the bay have been decreasing due to regulations in The Guiding Principel on Countermeasures for Eutrophication in Tokyo Bay in 1982 and Water Pollution Control Law in 1993. Despite the increases in nutrient levels, the spatial extention and duration of the Tokyo Bay hypoxia has been increasing. The Tokyo Bay is still eutrophic, suggesting that the nutrient loading reduction alone is not sufficient to improve the eutrophic conditions of the bay. The ability of Tokyo Bay to recycle nutrients has most likely deteriorated due to the substantial loss of tidal flats because of coastal reclamation.