Ultrafiltration with ceramic hollow fiber membranes was investigated by compressed sensing rapid acquisition relaxation enhancement (CS-RARE) magnetic resonance imaging (MRI) to characterize filtration mechanisms. Sodium alginate was used as a model substance for extracellular polymeric substances. Dependent on the concentration of divalent ions like Ca21 in an aqueous alginate solution, the characteristics of the filtration change from concentration polarization to a gel layer. The fouling inside the membrane lumen could be measured by MRI with a CS-RARE pulse sequence. Contrast agents have been used to get an appropriate contrast between deposit and feed. The lumen was analyzed quantitatively by exploring the membrane’s radial symmetry, and the resulting intensity could be modeled. Thus, different fouling mechanisms could be distinguished. CS-RARE-MRI was proven to be an appropriate in situ tool to quantitatively characterize the deposit formation during in-out filtration processes. The results were underlined by flux interruption experiments and length dependent studies, which make it possible to differentiate between gel layer or cake filtration and concentration polarization filtration processes.