Coastal waters contain substantial amounts of dissolved organic matter, a fraction of which contributes to organic alkalinity (OrgAlk) through proton-binding functional groups. However, OrgAlk is rarely considered explicitly in conventional carbonate system calculations, in which total alkalinity is often assumed to be entirely inorganic. Our observations from seven major estuaries in southern China show that OrgAlk occurs at substantial concentrations and can significantly influence seawater pH and buffering capacity. When total alkalinity is used as an input parameter, neglecting OrgAlk can therefore introduce substantial biases into calculated pH and pCO₂. This issue is also highly relevant to ocean alkalinity enhancement. Current assessments generally assume that added alkalinity is fully available to increase inorganic carbon storage and atmospheric CO₂ uptake, while treating total alkalinity as equivalent to inorganic alkalinity. Such an assumption may lead to substantial errors in estimates of effective alkalinity addition and CO₂ removal efficiency, particularly in organic carbon-rich coastal waters. We suggest that OrgAlk should be explicitly quantified and incorporated into carbonate system calculations and assessments of alkalinity enhancement in coastal waters and other aquatic systems where its influence is significant.