Bilge water is a complex mixture of various compounds from mechanical parts of ships. The effect of bilge water on a Biofilm-MBR process was investigated in this paper. When bilge water was included in the feed, the removal of total organic carbon in the biofilm reactor was not only depended on the biodegrading process but also gravity separation of oil emulsions. The removal of soluble organic compounds decreased with the increasing SDBS concentration. When bilge water was introduced to the Biofilm-MBR process, particle size distribution analysis of biomass was not enough to investigate membrane fouling and SDBS was the keystone of membrane performance and fouling. The membrane fouling rate increased with increasing SDBS concentration.