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Although the water quality in Hiroshima Bay has improved due to government measures, nutrient reduction has sharply decreased fisheries production. The law was revised in 2015, where the nutrient effluents from the sewage treatment plants were relaxed, yet no increase in fishery production was observed. Herein, we investigate the distribution of C, N, S, and P within Hiroshima Bay. Material loads from land and oyster farming activity influenced the C and S distributions in the bay sediments, respectively. Natural denitrification caused N reduction in areas by the river mouths and the landlocked areas whose sediments are reductive. The P content was high in the areas under aerobic conditions, suggesting metal oxide-bound P contributes to P accumulation. However, it was low in the areas with reducing conditions, indicating P is released from the sediments when reacting with H₂S. In such reductive sediments, liberated H₂S also consumes dissolved oxygen causing hypoxia in the bottom layer. It was estimated that 0.28 km³ of muddy sediment and 1.8 × 10⁵ ton of P accumulated in Hiroshima Bay. There remains conflict between the ‘Legacy of Eutrophication’ in the sediment and ‘Cultural Oligotrophication’ in the surface water due to 40 years of reduction policies.