Oxygen depletion in estuaries is a worldwide problem with detrimental effects on many organisms. Although nutrient loading has been stabilized for a number of these systems, seasonal hypoxia persists and displays large year‐to‐year variations, with larger hypoxic volumes in wetter years and smaller hypoxic volumes in drier years. Data analysis points to climate as a driver of interannual hypoxia variability, but nutrient inputs covary with freshwater flow. Here we report an oxygen budget analysis of Chesapeake Bay to quantify relative contributions of physical and biogeochemical processes. Vertical diffusive flux declines with river discharge, whereas longitudinal advective flux increases with river discharge, such that their total supply of oxygen to bottom water is relatively unchanged. However, water column respiration exhibits large interannual fluctuations and is correlated with primary production and hypoxic volume. Hence, the model results suggest that nutrient loading is the main mechanism driving interannual hypoxia variability in Chesapeake Bay.

Climate change is known to cause deoxygenation in the open ocean, but its effects on eutrophic and seasonally hypoxic estuaries and coastal oceans are less clear. Using Chesapeake Bay as a study site, we conducted climate downscaling projections for dissolved oxygen and found that the hypoxic and anoxic volumes would increase by 10‐30% between the late 20^th and mid‐21^st century. A budget analysis of dissolved oxygen in the bottom water revealed differing physical and biogeochemical responses to climate change. Sea level rise and larger winter‐spring runoff led to stronger stratification and large reductions in the vertical oxygen supply to the bottom water. On the other hand, warming led to earlier initiation of hypoxia, accompanied by weaker summer respiration and more rapid termination of hypoxia. Decreasing solubility due to warming accounted for about 50% of the reduction in the bottom water oxygen content.

The study of acidification in Chesapeake Bay is challenged by the complex spatial and temporal patterns of estuarine carbonate chemistry driven by highly variable freshwater and nutrient inputs. A new module was developed within an existing coupled hydrodynamic‐biogeochemical model to understand the underlying processes controlling variations in the carbonate system. We present a validation of the model against a diversity of field observations, which demonstrated the model's ability to reproduce large‐scale carbonate chemistry dynamics of Chesapeake Bay. Analysis of model results revealed that hypoxia and acidification were observed to cooccur in midbay bottom waters and seasonal cycles in these metrics were regulated by aerobic respiration and vertical mixing. Calcium carbonate dissolution was an important buffering mechanism for pH changes in late summer, leading to stable or slightly higher pH values in this season despite persistent hypoxic conditions. Model results indicate a strong spatial gradient in air‐sea CO₂ fluxes, where the heterotrophic upper bay was a strong CO₂ source to atmosphere, the mid bay was a net sink with much higher rates of net photosynthesis, and the lower bay was in a balanced condition. Scenario analysis revealed that reductions in riverine nutrient loading will decrease the acid water volume (pH < 7.5) as a consequence of reduced organic matter generation and subsequent respiration, while bay‐wide dissolved inorganic carbon (DIC) increased and pH declined under scenarios of continuous anthropogenic CO₂ emission. This analysis underscores the complexity of carbonate system dynamics in a productive coastal plain estuary with large salinity gradients.

The carbon cycle in estuarine environments is difficult to quantify because of substantial spatiotemporal heterogeneity in the sources, exchanges, and fates of carbon. We overcame these challenges with a multidecade numerical modeling analysis of seasonal, interannual, and decadal variability in net ecosystem metabolism (NEM) and associated carbon fluxes in Chesapeake Bay. Interannual variability in NEM along the estuarine axis indicated a clear spatial dependency of NEM on riverine discharge, with elevated flows causing increasing upper bay heterotrophy and increasing lower bay autotrophy during wet years. Our 30‐year simulation suggested the Chesapeake Bay is somewhat unique among estuaries in its tendency toward net autotrophy as a consequence of its extremely high nutrient to organic matter input ratio and large size. Budgets of three different carbon pools revealed that the entire Chesapeake Bay is a CO₂ source to the atmosphere and organic carbon source to the open shelf, providing quantitative export estimates for interpretation of anthropogenic perturbations to the regional carbon flux.

Tropical Storm Lee (2011) caused a record flood in the Susquehanna River which discharged about 6.7 million tons of suspended sediments into the Bay, an amount equal to the input of 6 average years. The flood‐carried sediment produced a large sediment plume that covered one half of Chesapeake Bay with the maximum suspended sediment concentration exceeding 2500 mg L⁻¹. Three stages were identified in the development of the sediment plume, corresponding to three dominant forcing mechanisms, i.e., river flow, estuarine circulation, and sediment settling. Most of the flood‐carried sediments were deposited in the Bay within 20 days. Sands were dumped in the Susquehanna Flats with a maximum thickness of 10 cm, while fine‐grained sediments were dusted over a wide area in the upper Bay with a maximum thickness of 4 cm. Long‐term simulation of the post‐storm period showed that a majority of the flood sediments were redistributed to accumulate in the estuarine turbidity maximum region due to flood–ebb asymmetry in tidal suspension and advection by estuarine circulation and tidal flows while the rest were transported seaward and deposited in the mid‐Bay. It is estimated that the flood delivered 9 months of particulate nitrogen and over 1 year of particulate phosphorus supplies to the estuary. This catastrophic event may change the geological history and exacerbate water‐quality decline in the American largest estuary.