The combined effects of anthropogenic and biological CO2 inputs may lead to more rapid acidification in coastal waters compared to the open ocean. It is less clear, however, how redox reactions would contribute to acidification. Here we report estuarine acidification dynamics based on oxygen, hydrogen sulfide (H2S), pH, dissolved inorganic carbon and total alkalinity data from the Chesapeake Bay, where anthropogenic nutrient inputs have led to eutrophication, hypoxia and anoxia, and low pH. We show that a pH minimum occurs in mid-depths where acids are generated as a result of H2S oxidation in waters mixed upward from the anoxic depths. Our analyses also suggest a large synergistic effect from river–ocean mixing, global and local atmospheric CO2 uptake, and CO2 and acid production from respiration and other redox reactions. Together they lead to a poor acid buffering capacity, severe acidification and increased carbonate mineral dissolution in the USA’s largest estuary.

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.

Few estuaries have inorganic carbon datasets with sufficient spatial and temporal coverage for identifying acidification baselines, seasonal cycles and trends. The Chesapeake Bay, though one of the most well-studied estuarine systems in the world, is no exception. To date, there have only been observational studies of inorganic carbon distribution and flux in lower bay sub-estuaries. Here, we address this knowledge gap with results from the first complete observational study of inorganic carbon along the main stem. Dissolved inorganic carbon (DIC) and total alkalinity (TA) increased from surface to bottom and north to south over the course of 2016, mainly driven by seasonal changes in river discharge, mixing, and biological carbon dioxide (CO 2 ) removal at the surface and release in the subsurface. Upper, mid-and lower bay DIC and TA ranged from 1000-1300, 1300-1800, and 1700-1900 µmol kg −1 , respectively. The pH range was large, with maximum values of 8.5 at the surface and minimums as low as 7.1 in bottom water in the upper and mid-bay. Seasonally, the upper bay was the most variable for DIC and TA, but pH was more variable in the mid-bay. Our results reveal that low pH is a continuing concern, despite reductions in nutrient inputs. There was active internal recycling of DIC and TA, with a large inorganic carbon removal in the upper bay and at salinities < 5 most months, and a large addition in the mid-salinities. In spring and summer, waters with salinities between 10 and 15 were a large source of DIC, likely due to remineralization of organic matter and dissolution of CaCO 3 . We estimate that the estuarine export flux of DIC and TA in 2016 was 40.3 ± 8.2 × 10 9 mol yr −1 and 47.1 ± 8.6 × 10 9 mol yr −1 . The estuary was likely a large sink of DIC, and possibly a weak source of TA. These results support the argument that the Chesapeake Bay may be an exception to the long-standing assumption that estuaries are heterotrophic. Furthermore, they underline the importance of large estuarine systems for mitigating acidification in coastal ecosystems, since riverine chemistry is substantially modified within the estuary.

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

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