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.

Ocean acidification (OA) is often defined as the gradual decline in pH and aragonite saturation state (Ω_Ar) for open ocean waters as a result of increasing atmospheric pCO₂. Potential long‐term trends in pH and Ω_Ar in estuarine environments are often obscured by a variety of other factors, including changes in watershed land use and associated riverine carbonate chemistry and estuarine ecosystem metabolism. In this work, we investigated the anthropogenic impacts on pH and Ω_Ar over three decades (1986–2015) in Chesapeake Bay using retrospective coupled hydrodynamic‐biogeochemical model simulations. Simulation results demonstrated a clear estuarine acidification signal in the midbay region, with a long‐term increase in the annual duration of acidified bottom waters (pH < 7.5, ~2 days/yr) as well as a shallowing of the saturation horizon (~0.1 m/yr). In contrast, scenario results revealed basification in the upper bay consistent with increased alkalinization of the Susquehanna River. Significant long‐term pH and Ω_Ar declines in the lower bay were driven by nearly equal contributions from OA and lowered surface ecosystem production. The midbay pH variability was primarily influenced by OA and biological processes, while river basification along with OA played a key role in regulating the long‐term Ω_Ar variability. This study quantifies the contributions from multiple anthropogenic drivers to changes in estuarine carbonate chemistry over three decades, highlighting the complex interactions in regulating the dynamics of pH and Ω_Ar and informing regional natural resource management and ecosystem restoration.