Total alkalinity (AT) is an important parameter in the study of aquatic biogeochemical cycles, chemical speciation modeling, and many other important fundamental and anthropogenic (e.g., industrial) processes. We know little about its short‐term variability, however, because studies are based on traditional bottle sampling typically with coarse temporal resolution. In this work, an autonomous AT sensor, named the Submersible Autonomous Moored Instrument for Alkalinity (SAMI‐alk), was tested for freshwater applications. A comprehensive evaluation was conducted in the laboratory using freshwater standards. The results demonstrated excellent precision and accuracy (± 0.1%–0.4%) over the AT range from 800 to 3000 μmol L−1. The system had no drift over an 8 d test and also demonstrated limited sensitivity to variations in temperature and ionic strength. Three SAMI‐alks were deployed for 23 d in the Clark Fork River, Montana, with a suite of other sensors. Compared to discrete samples, in situ accuracy for the three instruments were within 10–20 μmol L−1 (0.3–0.6%), indicating good performance considering the challenges of in situ measurements in a high sediment, high biofouling riverine environment with large and rapid changes in temperature. These data reveal the complex AT dynamics that are typically missed by coarse sampling. We observed AT diel cycles as large as 60–80 μmol L−1, as well as a rapid change caused by a runoff event. Significant errors in inorganic carbon system modeling result if these short‐term variations are not considered. This study demonstrates both the feasibility of the technology and importance of high‐resolution AT measurements.

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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.