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Coastal and estuarine systems play an important role in the global carbon cycle and often have complex carbonate chemistry dynamics due to a multitude of biogeochemical and physical drivers. Compared to classic estuaries, mechanisms driving the distribution of carbonate parameters in low-inflow estuaries are understudied. The spatial distribution of carbonate chemistry and hydrodynamic parameters were characterized in Morro Bay, a short and seasonally hypersaline estuary on the Central California Coast, during the dry, low-inflow season to better understand in situ modifications. Sampling transects were completed in the main channel in June, August, and September of 2018, bracketing both a high and low tide on each date. Temperature, salinity, total alkalinity, and dissolved inorganic carbon all increased from the mouth to the back of the estuary, with larger values observed during the low tide. pH values decreased towards the back of the bay, and had little variation between high and low tide for June and August transects. Flushing times (estimated using a salt-budget model approach) also increased toward the back of the bay which led to hypersaline conditions. Salinity alone only explained 20–33% of observed changes in total alkalinity and 13–22% of observed changes in dissolved inorganic carbon throughout the bay. The remaining changes in total alkalinity and dissolved inorganic carbon were likely driven by biogeochemical modifications enhanced by extended flushing times, particularly in the back bay. Prior to this project, Morro Bay experienced a recent, rapid collapse of eelgrass, the major biogenic habitat. In the last four years eelgrass in Morro Bay appears to be on a recovery trajectory; therefore, this study provides a baseline whereby future studies can evaluate carbonate chemistry changes associated with potential eelgrass recovery and expansion. This study highlights the unique hydrodynamic exchange in seasonally low-inflow estuaries and its potentially large role in influencing local carbonate chemistry and ocean acidification. • Hydrodynamic exchange in low-inflow estuaries influences local carbonate chemistry. • Large tidal differences in alkalinity due to hypersaline conditions near bay head. • Flushing time largely explains spatial trends in carbonate chemistry. • Diel cycles and long flushing times minimized tidal differences in dissolved CO 2. [ABSTRACT FROM AUTHOR]