In membrane bioreactors applied to wastewater treatment, fouling is typically a complex function of sludge characteristics. A pilot-scale tertiary submerged membrane bioreactor (tMBR) was continuously operated for over 200 days to assess the effect of biomass physiological state and environmental stress on process performance. Sludge characteristics were evaluated in terms of suspended solid concentration (MLSS and MLVSS), apparent viscosity, bioflocculation state, filterability, bioactivity, biopolymeric clusters (BPCs) and soluble microbial products. During the initial period of the tMBR start-up, when MLSS was below 3000 mg/L, the biomass was found to be very sensitive to environmental stress by sudden oxygen increase or organic shock loading, resulting in temporary biomass deflocculation and BPC release, and consequently, severe induced membrane fouling. However, at higher MLSS values, low stable biomass growth (0.04 ± 0.002 kg MLVSS/kg COD) was measured, regardless of organic overloading shocks or feeding failures. This period was also characterised by low bioactivity, BPC content and membrane fouling. Statistical analysis showed that BPCs have an important role when compared with other sludge properties as indicators of its fouling potential.