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Abstract Variations in estuarine carbonate chemistry can have critical impacts on marine calcifying organisms, yet the drivers of this variability are difficult to quantify from observations alone, due to the strong spatiotemporal variability of these systems. Terrestrial runoff and wetland processes vary year to year based on local precipitation, and estuarine processes are often strongly modulated by tides. In this study, a 3D-coupled hydrodynamic-biogeochemical model is used to quantify the controls on the carbonate system of a coastal plain estuary, specifically the York River estuary. Experiments were conducted both with and without tidal wetlands. Results show that on average, wetlands account for 20–30% of total alkalinity (TA) and dissolved inorganic carbon (DIC) fluxes into the estuary, and double-estuarine CO₂outgassing. Strong quasi-monthly variability is driven by the tides and causes fluctuations between net heterotrophy and net autotrophy. On longer time scales, model results show that in wetter years, lower light availability decreases primary production relative to biological respiration (i.e., greater net heterotrophy) resulting in substantial increases in CO₂outgassing. Additionally, in wetter years, advective exports of DIC and TA to the Chesapeake Bay increase by a factor of three to four, resulting in lower concentrations of DIC and TA within the estuary. Quantifying the impacts of these complex drivers is not only essential for a better understanding of coastal carbon and alkalinity cycling, but also leads to an improved assessment of the health and functioning of coastal ecosystems both in the present day and under future climate change. 

Estuarine environments are characterized by strong spatial gradients and high temporal variability that are difficult to fully capture with discrete field measurements. This is particularly the case in the Chesapeake Bay, the largest estuary in the continental United States. This archive provides a climatological atlas of physical and biogeochemical conditions for the Chesapeake Bay based on numerical model results of 1985-2023. The atlas includes surface and bottom conditions on a fine longitude/latitude grid with a monthly frequency. The environmental variables are stored in a NetCDF file with abundant metadata that can be used in software such as QGIS, Python, R, Matlab or GNU Octave. A 50+ page documentation in PDF format provides additional information on the environmental variables, the numerical model used to generate the climatology, and an evaluation of the model skill over the period of the atlas. The documentation also includes ready-made visualizations for each environmental variable.