The goal of this study was to evaluate the effect of mixing intensity on the aggregation of Fe and Fe–Mn oxides and the structure and composition of these oxides on membrane fouling. The size and fractal dimension of oxides were determined by a particle sizer with small-angle static laser scattering (SALLS) before each membrane filtration test. The performance of membrane filtration was evaluated by relative flux and mean flux, while the fouling was analyzed by fouling resistance. In addition, the contact angle of the cake was also measured by the sessile drop method, to determine the hydrophobicity of the cake.