<p>The aim of this study is to develop, combine, and optimize a three-dimensional water quality and sediment transport model with a bed module. This bed model incorporates a layered model that defines both dissolved and solid phases in vertically layered dimensions. To calibrate the integrated model, a comprehensive dataset consisting of water quality parameters in Tokyo Bay (Japan) was utilized. Tokyo Bay is known for its heavy eutrophication, which results in the accumulation of soft-organic sediment in inner parts, particularly near the head of the bay. One key focus of this study was to investigate near-bed–water conditions and their impact on oxygen depletion, nutrient cycling, primary production, and overall water quality. The results obtained from simulating particulate organic carbon content ratio on the sediment surface were found to be consistent with observed values. Additionally, accurate simulations of other water quality parameters were successfully achieved using this developed model. This developed model proves to be a valuable tool for future studies aimed at improving environmental management strategies within Tokyo Bay. The sophisticated modeling of hypoxic and anoxic conditions in inner parts of the bay, which pose chronic threats to benthic life and severely deteriorate water quality, provides valuable insights for analyzing the consequences of various scenarios related to anthropogenic actions. This model can assist researchers and policymakers in making informed decisions regarding environmental management strategies within Tokyo Bay.</p>