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.

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.

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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 20th and mid-21st 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.

ince the industrial revolution, the global ocean has absorbed approximately 30% of the anthropogenic CO 2 emissions from the atmosphere, lowering the average surface ocean water pH by 0.1 units and aragonite carbonate mineral saturation state (Ω arag ) by 0.5 units. This process, known as ocean acidification 1,2 , is harmful to some marine organisms and ecosystems 3 . In coastal waters, acidification is enhanced by eutrophication and the subsequent hypoxia and anoxia via the accumulation of CO 2 and acids below the pycnocline 4,5 . Calcium carbonate (CaCO 3 ) mineral dissolution can increase the total alkalinity (TA) of water, and is proposed as a buffer to neutralize anthropogenic CO 2 uptake 6,7 . Recent studies have shown that CaCO 3 dissolution can offset a notable proportion of the metabolic CO 2 and increase survivorship of juvenile bivalves, thus providing a substantial negative feedback to coastal acidification 8,9 .However, very few studies have linked CaCO 3 dissolution to the timing and location of its formation in coastal waters 10,11 as a corollary to the ocean's carbonate counter pump 11 . These dynamic links are essential to understand given their capacity to mediate aquatic pH and atmospheric CO 2 concentrations 8,12 . In coastal waters, CaCO 3 can be formed via abiotic precipitation or biotic production, which are usually associated with coral reefs, calcareous algae 13 , molluscs 14 , bacteria 15 , fish 16 and aquatic plants 17 . Recently, seagrass meadows have been shown to be major sites for CaCO 3 accumulation and storage in high-salinity waters in equatorial and subtropical regions 18 . In addition to calcification from the seagrass-calcifying algae, infauna and epibiont community, the seagrass Thalassia testudinum