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Abstract There is limited information on how the nutrient and freshwater input affects water column carbonate chemistry in the estuaries along the northern Gulf of Mexico. In this study, we assess the seasonal and spatial variability in carbonate chemistry in the Barataria Basin, a eutrophic estuary adjacent to the mouth of the Mississippi River. Eleven stations were sampled along a salinity gradient during the winter (January), spring (April), summer (July), and fall (October) of 2021. Surface and bottom water samples were collected for the analyses of dissolved inorganic carbon (DIC); total alkalinity (TA); and nitrite plus nitrate (NO₂ + NO₃), phosphate (PO₄), and dissolved silica (SiO₄). Dissolved CO₂(pCO₂) was measured in the surface water. Seasonal surface DIC and TA values ranged from 1553 to 2582 μmol kg⁻¹and 1217 to 2217 μmol kg⁻¹, respectively. DIC and TA varied seasonally and showed an increasing trend from fresh stations to saline stations. The highest DIC and TA values were observed during the fall season, likely due to the increased contribution of DIC and TA from adjacent marshes as a result of enhanced porewater exchange. In contrast to DIC and TA, pCO₂decreased with the increase of salinity. The seasonal and spatial patterns in carbonate chemistry could not be explained solely by physical mixing and reflected complex interactions between biogeochemical processes driven by nutrient supply and temperature as well as tidal flushing and material exchanges with adjacent marshes.