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We measured the carbonate system (between 2015 and 2018) in an isolated and a well‐connected temperate estuary, both known for shellfish growth. We evaluated end‐member model estimates of inorganic carbon, alkalinity, pH, mineral saturation states (Ωa), and pH sensitivity (βDIC). We find winter conditions are estimated within observational uncertainty. Spring‐summer primary productivity elevates observed pH and Ωa above theoretical lines, beyond uncertainty. Both estuaries are sensitive in winter and likely to experience rapid pH changes with increased inorganic carbon inputs. Summer pH sensitivity is reduced by productivity and is least sensitive in the midsalinity region. We estimate carbon increased by up to 49 μmol kg−1, since the pre‐industrial period resulting in significant decreases in pH (0.2) and Ωa (0.5). The largest pH decrease occurred outside the minimum buffer zone, at higher salinities where carbon increase was greatest. The largest pH decrease occurred in winter, but the largest Ωa decrease occured in summer. Plain Language Summary: The ocean has absorbed about a third of human carbon dioxide emissions, increasing its acidity. Increasing acidity negatively affects marine organisms such as shellfish and fish that build calcium carbonate structures because they must spend more energy building and maintaining these structures. Most farmed and wild shellfish live in estuarine environments where acidification has not been widely studied. We made complete carbon system measurements over several years and across all seasons, in two distinct estuaries with significant aquaculture, where no previous carbon data existed. We estimated key acidification parameters and evaluated our ability to predict these parameters using only salinity, once properties in the freshest and saltiest water in the systems were well defined in all seasons. Our simple "mixing model" estimates winter conditions well, but during summer, phytoplankton blooms take up carbon and make conditions more favorable than predicted. We found that both estuaries are sensitive to future increases in carbon and are likely to experience rapid changes in chemistry. We estimate that human activity has already caused significant increases in inorganic carbon and associated acidification. The largest change critical to shell‐building organisms has occurred during the summer, and at higher salinities that are typical of grow sites. Key Points: End‐member mixing estimates winter pH and mineral saturation states in temperate estuaries within measurement uncertaintySeasonal productivity keeps pH and mineral saturation states above theoretical mixing curves by up to ∼1 pH and ∼2.5 Ωa, respectivelySince the preindustrial period nearshore estuarine pH declined by 0.05–0.2 with largest decline outside the minimum buffer zone [ABSTRACT FROM AUTHOR]