Mobile Bay, a microtidal, shallow, and stratified estuary in the northern Gulf of America, receives substantial discharge and nutrient loading from the watershed and has been prone to hypoxia for over a century. Besides the generic features of the other microtidal estuaries exhibiting weak tidal mixing, Mobile Bay’s uniqueness of having human-engineered navigation channels, which are 4-5 times deeper than the natural bathymetry, also regulates dynamics in the system. Recent studies reveal that continuous deepening and widening of the channel increase bay-wide salinity but reduce stratification, yet the implications for dissolved-oxygen dynamics remain largely unresolved.
To address this knowledge gap, we employ a coupled physical-biochemical SCHISM-CGEM model (Semi Implicit Cross-scale Hydroscience Integrated System - Coastal Generalized Ecosystem Model) to simulate oxygen dynamics in Mobile Bay. SCHISM-CGEM integrates the efficiency of hydrodynamic simulations with advanced optical and sediment-diagnostics parameterizations in biochemical modeling tailored for shallow and turbid estuarine ecosystems for the first time. After validation with field observations, a series of scenario studies covering bathymetry in historic (1913) and present-day (2025) under combined factors, including varying river discharge and wind forcing, are conducted to quantify the effects of bathymetric change on estuary-wide oxygen content, hypoxia hotspots, area, volume, and duration, air-sea oxygen flux, and wind-driven reoxygenation. This systematic modeling study provides more profound
understanding of the sensitivity of water quality to anthropogenic modifications to bathymetry and offers guidance for coastal resource and navigation management.