Humic acid (HA) and fulvic acid (FA) are two operationally defined classes of natural organic matter. In the environment, both materials are present simultaneously and bind in a competitive manner to Fe-(hydr)oxides and other minerals, but their quantification in mixtures is a challenge. In this study, an UV–Vis method was developed to quantify concentrations of HA and FA without and after adsorptive fractionation by an iron oxide (goethite, α-FeOOH). In addition, the performance of the UV–Vis method was compared to that of acid precipitation and size exclusion chromatography (SEC). Among the three methodologies (UV–Vis, acid precipitation, SEC), the UV–Vis method is the most successful in quantifying the ratio of HA to FA subject to fractionation. The UV–Vis method is based on distinct differences in the UV–Vis spectra of HA and FA, including fingerprints in both the spectra shape and intensity. Adsorption to goethite decreased the specific light absorbance of HA and FA, but the changes in spectral shape were not significant enough to cover their differences. The acid precipitation method can also quantify the HA to FA ratio. But to minimize the influence of incomplete HA precipitation or co-precipitation of FA, the concentration of both HA and FA needs to be at least ~20 mgC L−1. The SEC method is not suitable to measure HA and FA after adsorption, because preferential adsorption significantly affects the shape of SEC chromatograms.