Sulfate is a critical component of schwertmannite. However, the sulfate content of schwertmannite decreases with the increase in AMD-polluted river pH value, and its impact on the surface properties and Cr(VI) adsorption of schwertmannite remains unclear. To address this issue, different methods, including batch adsorption, N2 physisorption, scanning electron microscopy (SEM), potentiometric titration, X-ray photoelectron spectroscopy (XPS), attenuated total reflectance–Fourier transform infrared spectroscopy (ATR-FTIR) in combination with two-dimensional correlation spectroscopy (2D-COS) analysis, and surface complexation modeling (SCM) were employed. Our results showed that sulfate existed as both non-protonated bidentate-binuclear complexes and non-protonated outer-sphere complexes in schwertmannite. The surface morphology and particle size of schwertmannite were unaffected by the sulfate content. However, a decrease in sulfate content resulted in a drop in the negative charge on the surface of schwertmannite, which is conducive to particle aggregation. An increase in pH, on the other hand, raised the negative charge and encouraged the dispersion of the particles. And then, reducing the sulfate content of schwertmannite led to a decrease in acid-base buffer and Cr(VI) adsorption capacity of schwertmannite. The adsorption process of Cr(VI) by schwertmannite can be divided into two stages. In the first stage, Cr(VI) was adsorbed primarily through anion exchange reactions with the sulfate; however, the contribution of surface complexation gradually increased as the initial sulfate content decreased because of a reduced likelihood of anion exchange and an increase in the specific surface area of schwertmannite. Additionally, the behavior of sulfate and Cr(VI) in this stage could be predicted based on the initial sulfate content of schwertmannite. In the second stage, surface complexation with hydroxyl sites became the predominant mechanism of adsorption, which still exhibited great potential at higher Cr(VI) concentrations. Finally, the aforementioned hypothesis was used to establish a CD-MUSIC model, and the fitting results demonstrated that the density and Cr(VI) adsorption capacity of the sulfate site dropped as the sulfate content decreased, while the hydroxyl site was less impacted. The findings have provided insights into further understanding the properties of schwertmannite and its adsorption of Cr(VI).