Fouling during coagulation–ceramic microfiltration of natural organic matter was investigated. Two process configurations (inline coagulation (IC) and tank coagulation (TC)) and two process conditions (types of coagulants–aluminum-based PAX and iron-based PIX–and G-values) were studied. The rate of irreversible fouling corresponding to the increase of initial transmembrane pressure after backwash of IC-PAX was lowest followed by TC-PAX and TC-PIX, while the performance of IC-PIX was found worst. The 1D and 2D fractal analysis revealed that flocs from IC were morphologically different from those of TC, leading to different filtration characteristics. The 3D fractal analysis revealed two groups of morphologically similar flocs: one led to successful filtration experiments, whereas the other led to unsuccessful ones. Cake porosity was found dependent on the floc morphology. Thus, such an approach was found complementary with fouling analysis by means of a membrane fouling model and minimization of fouling phenomenon was achieved by combining the two approaches.