Abstract. Total alkalinity (TAlk) has long been used to evaluate the buffering capacity of aquatic systems. TAlk has also been used, together with measurements of either pH or dissolved inorganic carbon (DIC), to indirectly estimate the partial pressure of carbon dioxide (pCO2) in inland waters, estuaries, and marine systems. These estimates typically assume that carbonate and bicarbonate ions comprise nearly all the species contributing to TAlk; however, other inorganic and organic acids have the potential to contribute significant non-carbonate alkalinity. To evaluate the potential for error in using TAlk to estimate pCO2, we measured pH, TAlk, and DIC in samples of river water. Estimates of pCO2 derived from TAlk and pH measurements were higher than pCO2 estimates derived from DIC and pH by 13–66%. We infer that this overestimate is due to the presence of significant non-carbonate alkalinity (NC-Alk). This study also describes the relative proportions of carbonate- and non-carbonate alkalinity measured in 15 river systems located in northern New England (USA) and New Brunswick (Canada). NC-Alk represents a significant buffering component in these river systems (21–∼100% of TAlk), and failure to account for NC-Alk (which cannot directly contribute to pCO2) leads to the overestimation of carbon dioxide release to the atmosphere.