Fouling of membranes in water treatment processes can be caused by the precipitation of inorganic salts, the accumulation of organic substances like polysaccharides, the deposition of organic and inorganic particles as well as the formation of microbial biofilms. The aim of this study was the reproducible generation of membrane deposits and their subsequent visualization by confocal laser scanning microscopy (CLSM). Model foulants were bacterial cells (Pseudomonas fluorescens) labeled with the DNA-binding dyes SYTO 62 or 4',6-diamidino-2-phenylindole, the synthetic clay laponite RD stained with the fluorescent dye rhodamine 6G, fluorescent carboxylate-modified polystyrene microspheres as well as the polysaccharide dextran labeled with fluorescein isothiocyanate. Mixtures of fluorescently labeled foulants were filtered through a polyethersulfone ultrafiltration membrane. CLSM in combination with image analysis allowed the three-dimensional reconstruction of the membrane deposits and the localization of each single foulant within the membrane deposits. This approach was applied to the visualization of cleaning effects on fouled membranes that had been treated by ultrasound in such a way that only partial removal of the deposits was achieved. By means of CLSM, uncleaned, weakly cleaned and completely cleaned areas could be detected on the membrane surface, so that the extent of ultrasound-induced membrane cleaning could be localized. In conclusion, CLSM in combination with image analysis proved suitable to visualize the three-dimensional distribution of fluorescently labeled foulants in multi-layered deposits and to evaluate the efficiency of cleaning measures for deposit removal.