Influence of substrate type (synthetic (SWW) or real wastewater (RWW)) on lab scale MBR performances (e.g. COD and N-NH4+ removal rates and bioactivities) was assessed. Membrane fouling was related to MBR biological medium characteristics. With RWW, autotrophic biomass was better acclimated with complete ammonium removal. MBR biological medium was characterized by main soluble microbial products (SMP) (proteins, polysaccharides and humic-like substances) quantification and molecular weights (MW) distribution determination. The biological medium of SWW acclimation contained 60 mg L (1) more of SMP, mainly composed of proteins and polysaccharides. A protein fraction having high MW (>600 kDa) could be responsible for higher removable fouling fraction in that case. SMP of RWW experiment were mainly composed of small proteic and humic-like fractions, poorly retained by the membrane and resulting in a weak augmentation of irremovable and irreversible fouling fractions compared to SWW acclimation. Therefore RWW utilization is preferable to approach real operating MBR.