Fouling is a major problem in membrane processes of water treatment. It can be caused by the deposition of inorganic and organic particulate material, and of microbial cells which may subsequently form biofilms. In practice, usually more than one foulant participates in the formation of membrane deposits. Knowledge of the composition of fouling layers is important for the development of appropriate countermeasures. For this purpose, an experimental system was established for the generation and microscopic visualisation of mixed deposits, using fluorescently labelled model foulants: (i) drinking-water bacteria stained with nucleic acid-specific dyes (biofouling), (ii) synthetic clay mineral laponite stained with rhodamine 6G (inorganic particle fouling), and (iii) fluorescently labelled polystyrene microspheres (organic particle fouling). Polycarbonate and polyethersulfone membranes were challenged with these foulants by dead-end filtration. On the basis of different fluorescent labels, the single foulants in these mixed deposits could be visualised separately by confocal laser scanning microscopy which, in combination with image analysis, allowed the generation of three-dimensional views of the complete deposits. This method offers the possibility for the estimation of quantitative surface coverage by foulants and for the determination of the efficacy of cleaning measures with respect to the removal of different foulants.