Two different sulfonephthalein indicators, cresol red (CR) with a pK a of ∼8.3 and bromothymol blue (BTB) with pKa of ∼7.4, were tested for an analysis of freshwater over a broad range of pH and total alkalinity values. Measurements from an autonomous sensor system using a 1 cm optical path length were compared to those using a 10 cm path length on a benchtop spectrophotometer. The indicator pH perturbation was quantified with a thermodynamic model and nonlinear least-squares analysis. The laboratory study found that the perturbation-corrected pH differed between the 1 cm (large indicator perturbation) and 10 cm (small indicator perturbation) optical path length measurements from -0.017 to +0.15 with a median of +0.0041 pH units for CR and from -0.015 to +0.026 with a median of -0.0008 pH units for BTB. Precision was ±0.0005-0.013 and ±0.0001-0.0027 pH units for the 1 and 10-cm-path-length measurements, respectively. The autonomous sensor was deployed for 14 days in a local creek. Simultaneous glass pH electrode measurements had a large negative and drifting offset (-0.15 to -0.40 pH units) compared to the indicator-based measurements. This study is the first in situ comparison between potentiometric and spectrophotometric pH methods in a freshwater system.