Estuaries and coastal areas connect the terrestrial and oceanic environments, and are essential for both marine economy and ecosystem. Hangzhou Bay located in the east coast of China and is known as its macro-tides and high turbidity. In this study, a three-dimensional numerical model, coupling tide-wave-sediment-ecology, is established and validated using field data in both calm and extreme weather conditions. The impacts of sediment on the key parameters of ecosystem are studied using the numerical model and field data. The model reveals a gradient in dissolved oxygen concentration (DOC), decreasing from north to south at the surface and from northwest to southeast at the bottom, with higher concentrations in the open sea compared to coastal areas. Particularly, the southeast area of the Zhoushan sea exhibits lower DOC, leading to frequent hypoxic conditions at the bottom. DOC levels show fluctuations corresponding with tidal cycles and seasonal variations, peaking in winter due to diminished microbial activity and increased oxygen solubility at lower temperatures. Numerical model results indicate that during summer, pronounced water stratification forms a distinct pycnocline, which reduces vertical mixing and contributes to oxygen depletion in bottom waters. Wind-induced mixing disrupts this stratification, facilitating the vertical circulation of oxygen-rich surface waters into deeper, oxygen-poor layers, thereby elevating the bottom DOC. Temperature also significantly influences DOC distribution by affecting both oxygen solubility and the rates of biogeochemical processes.