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Abstract The capacity of aquatic systems to buffer acidification depends on the sum contributions of various chemical species to total alkalinity (TA). Major TA contributors are inorganic, with carbonate and bicarbonate considered the most important. However, growing evidence shows that many rivers, estuaries, and coastal waters contain dissolved organic molecules with charge sites that create organic alkalinity (OrgAlk). This study describes the first comparison of (1) OrgAlk distributions and (2) acid–base properties in contrasting estuary‐plume systems: the Pleasant (Maine, USA) and the St. John (New Brunswick, CA). The substantial concentrations of OrgAlk in each estuary were sometimes not conservative with salinity and typically associated with very low pH. Two approaches to OrgAlk measurement showed consistent differences, indicating acid–base characteristics inconsistent with the TA definition. The OrgAlk fraction of TA ranged from 78% at low salinity to less than 0.4% in the coastal ocean endmember. Modeling of titration data identified three groups of organic charge sites, with mean acid–base dissociation constants (pK_a) of 4.2 (± 0.5), 5.9 (± 0.7) and 8.5 (± 0.2). These represented 21% (± 9%), 8% (± 5%), and 71% (± 11%) of titrated organic charge groups. Including OrgAlk, pK_a, and titrated organic charge groups in carbonate system calculations improved estimates of pH. However, low and medium salinity, organic‐rich samples demonstrated persistent offsets in calculated pH, even using dissolved inorganic carbon and CO₂partial pressure as inputs. These offsets show the ongoing challenge of carbonate system intercomparisons in organic rich systems whereby new techniques and further investigations are needed to fully account for OrgAlk in TA titrations. 

Abstract Estuaries may be uniquely susceptible to the combined acidification pressures of atmospherically driven ocean acidification (OA), biologically driven CO 2 inputs from the estuary itself, and terrestrially derived freshwater inputs. This study utilized continuous measurements of total alkalinity (TA) and the partial pressure of carbon dioxide (pCO 2 ) from the mouth of Great Bay, a temperate northeastern U.S. estuary, to examine the potential influences of endmember mixing and biogeochemical transformation upon estuary buffering capacity ( β – H ). Observations were collected hourly over 28 months representing all seasons between May 2016 and December 2019. Results indicated that endmember mixing explained most of the observed variability in TA and dissolved inorganic carbon (DIC), concentrations of which varied strongly with season. For much of the year, mixing dictated the relative proportions of salinity‐normalized TA and DIC as well, but a fall season shift in these proportions indicated that aerobic respiration was observed, which would decrease β – H by decreasing TA and increasing DIC. However, fall was also the season of weakest statistical correspondence between salinity and both TA and DIC, as well as the overall highest salinity, TA and β – H . Potential biogeochemically driven β – H decreases were overshadowed by increased buffering capacity supplied by coastal ocean water. A simple modeling exercise showed that mixing processes controlled most monthly changes in TA and DIC, obscuring impacts from air–sea exchange or metabolic processes. Advective mixing contributions may be as important as biogeochemically driven changes to observe when evaluating local estuarine and coastal OA.