Inland waters have an important role in the global carbon cycle, contributing significantly to terrestrial carbon fluxes through downstream export and exchange of CO2 with the atmosphere. However, large uncertainties in freshwater inorganic carbon fluxes remain. One contributing factor is uncertainty in carbonate system calculations for estimating the partial pressure of CO2 (pCO2) from pH and alkalinity in freshwater systems. The uncertainty stems largely from inaccurate pH values caused by glass pH electrode measurements in low ionic strength systems. This study compares indicator-based spectrophotometric and electrochemical pH measurements and their application for calculating freshwater pCO2. Our study found that, compared to a pCO2 reference method, pH electrode-based estimates of pCO2 were overestimated by 230 ± 200 μatm (n = 54) where indicator-based spectrophotometric pH estimates of pCO2 were 58 ± 33 μatm (n = 34) over the range of 100–1600 μatm. Furthermore, we found that when ionic strength was assumed to be zero, calculated pCO2 error was ~ 20% of the reference pCO2. A 19-d field study using autonomous spectrophotometric pH and pCO2 sensors found an average error in calculated pCO2 of −70 ± 57 μatm (n = 1685). Although, our focus is on riverine CO2, these findings and subsequent conclusions apply to all freshwater systems. Spectrophotometric pH measurements will improve future freshwater pCO2 calculations and better quantify inland waters' role in the global carbon budget.