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Abstract The marine carbonate system is influenced by anthropogenic CO₂uptake, biogeochemical processes, and physical changes that involve freshwater input and removal. Two frequently used parameters to quantify seawater carbonate system are total alkalinity (TA) and total dissolved inorganic carbon (DIC). To account for the physical changes, both TA and DIC are usually normalized to a reference salinity (i.e., nTA and nDIC), and then the relationship between nTA and nDIC is used to identify major biogeochemical processes that regulate the carbonate system, based on process‐specific reaction stoichiometry. However, the theoretical basis of this interpretation has not been holistically examined. In this study, we validated this method under  idealized conditions and discussed the associated assumptions and limitations. Furthermore, we applied this method to interpret field TA and DIC data from a lagoonal estuary in the northwestern Gulf of Mexico. Our results demonstrated that evaluating field data that encompass multiple stations and time periods could be problematic. In addition, various combinations of biogeochemical processes can lead to the same nTA–nDIC relationship, even though the relative importance of each individual process may vary significantly. Therefore, the stoichiometric relationship relying solely on TA and DIC data is not a definitive approach for uncovering dominant biogeochemical processes. Instead, measurements of process‐specific parameters are necessary.