In three pilot plants in the Netherlands the performance of either nanofiltration or reverse osmosis in water treatment was studied. Operational problems observed in these systems, viz. increased normalized pressure drop (NPD) and/or declined normalized flux (MTC) values, were attributed to biofouling. To elucidate the role of biofouling, data were collected about biomass accumulation in the membrane elements applying destructive autopsies of the membrane units. Biomass parameters included: total direct cell counts (TDC), adenosinetriphosphate (ATP) analysis and heterotropic plate counts (HPC). Maximum values of biomass parameters at the feed side of the membranes were: 2.1 × 108 cells/cm2, 1.5 × 104 pg ATP/cm2 and 1.8 × 107 CFU/cm2, respectively. Microscopic observations of biomass obtained from the membrane systems indicated that the observed organisms were metabolically active in most cases. AOC levels in the feed water were relatively low. In one case, an increase had been observed following the addition of acid to prevent CACO3 scaling and also a high biofilm formation rate was observed in relation with a strong NPD increase. Cleaning agents tested under laboratory conditions and in practice did reduce ATP concentrations, but TDC values revealed that biomass removal from the membrane was very limited. These observations show that operational problems caused by biofouling are difficult to solve by cleaning. Therefore, biomass accumulation in membrane elements should be limited by: (i), achieving a far going removal of growth-promoting compounds and micro-organisms from the feedwater, (ii), securing the purity of the chemicals dosed, and (iii), applying effective cleaning procedures for biomass removal.