The global increase in coastal hypoxia over the past decades has resulted from a considerable rise in anthropogenically-derived nutrient loading. The spatial relationship between surface phytoplankton production and subsurface hypoxic zones often can be explained by considering the oceanographic conditions associated with basin size, shape, or bathymetry, but that is not the case where nutrient-enriched estuarine waters merge into complex coastal circulation systems. We investigated the physical and biogeochemical processes that create high-biomass phytoplankton production and hypoxia off the Changjiang (Yangtze River) Estuary in the East China Sea (ECS). Extensive in situ datasets were linked with a coupled Regional Ocean Modeling Systems (ROMS) and carbon, silicate, and nitrogen ecosystem (CoSiNE) model to explain the temporary decoupling of phytoplankton production and hypoxia. The CoSiNE model contains two functional groupings of phytoplankton—diatoms and “other”—and the model results show that diatoms were the major contributors of carbon export and subsurface hypoxia. Both observations and simulations show that, although surface phytoplankton concentrations generally were much higher above hypoxic zones, high-biomass distributions during the summer–fall period did not closely align with that of the bottom hypoxic zones. Model results show that this decoupling was largely due to non-uniform offshore advection and detachment of subsurface segments of water underlying the Changjiang River plume. The near-bottom water carried organic-rich matter northeast and east of the major hypoxic region. The remineralization of this particle organic matter during transit created offshore patches of hypoxia spatially and temporally separated from the nearshore high-biomass phytoplankton production. The absence of high phytoplankton biomass offshore, and the 1–8 weeks’ time lag between the surface diatom production and bottom hypoxia, made it otherwise difficult to explain the expanded core hypoxic patch and detached offshore hypoxic patches. The findings here highlight the value of developing integrated physical and biogeochemical models to aid in forecasting coastal hypoxia under both contemporary and future coastal ocean conditions.

Sediment oxygen consumption (SOC) is important in modulating the oxygen budget in the East China Sea where seasonal hypoxia occurs. Porewater advection, molecular diffusion and bioturbation supply oxygen for sedimentary organic matter degradation. A pelagic‐benthic coupled model was applied to quantify the SOC. A comparison with observations showed good model performance in reproducing the hydrographic and ecological environments, particularly for the interannual variation in the hypoxic zone. Simulation results show that porewater‐advection‐induced flux is the predominant component of the SOC in sandy areas on the Changjiang bank and outer shelves, while the bioturbation‐induced flux is predominant at mud depocenters. By comparing SOC to the water oxygen consumption (WOC) below the pycnocline, the contribution of SOC is generally below ∼40% in the hypoxic zone. The spatial distribution of SOC in summer is relatively steady from year to year, while the high WOC patches explain more about the interannual variation in the hypoxic zone. WOC rather than SOC drives the variation of hypoxia. Particularly on the Changjiang bank, milder hydrodynamics are favorable for both the higher WOC and bioturbation‐induced benthic oxygen flux but substantially suppress the porewater advective flux, which results in the net lower contribution of SOC to hypoxia. This finding may shed light on other pelagic‐benthic coupling processes in coastal shelf seas where hypoxia occurs on permeable sediments.