Fouling layer formation in membrane processes and the role of bacteria in it were investigated using rRNA-targeted fluorescently labelled oligonucleotides. In a laboratory-scale flat-channel test unit, nano-and ultrafiltration of an oligotrophic reservoir water were performed. The bacterial composition of the primary fouling layer showed a dominance of the gamma-subclass of proteobacteria. The mature fouling layer was dominated by bacteria of the alpha- and beta-subclass, which was similar to the population structure of the raw water. The results indicate that in particular gamma-proteobacteria have attachment mechanisms to form the primary biofilm, which is then colonized by other bacteria. It could be shown that bacterial activity was high enough to obtain good fluorescence signals, though staining of active cells by a tetrazolium salt failed. Inorganic precipitation played a minor role in the fouling layer formation, while natural organic matter made up its main part. Scanning electron microscopy revealed both layer and pore fouling for the ultrafiltration membrane due to organic deposition.