The impact of removable and irremovable fouling on the retention of viral and bacterial indicators by the submerged microfiltration membrane in an MBR pilot plant was evaluated. Escherichia coli, sulphite-reducing Clostridium spores, somatic coliphages and F-specific RNA bacteriophages were used as indicators. The membrane demonstrated almost complete removal of E. coli and sulphite-reducing Clostridium spores. However, there was no correlation with membrane fouling. The phage removal varied in accordance with the irremovable fouling, rising from 2.6 to 5.6 log(10) units as the irremovable fouling increased (measured by the change in the transmembrane pressure). In contrast, removable fouling did not have any effect on the retention of viruses by the membrane. These results indicate that irremovable membrane fouling may affect the removal efficiency of MBRs and, therefore, their capacity to ensure the required microbiological standards for the permeate achieved. (C) 2011 Elsevier Ltd. All rights reserved.