The main objective of this work was to determine the impacts of various operational conditions and biomass characteristics on membrane fouling in a pilot-scale, submerged membrane bioreactor (MBR). Fouling behavior was studied at five different mixed liquor suspended solids (MLSS) concentrations and four different aeration velocities at each MLSS concentration. Concentrations of both protein and carbohydrate fractions of extracellular polymeric substances (EPS) and soluble microbial products (SMP) increased with increasing MLSS concentrations. The distribution of particle sizes shifted toward smaller particles and mean particle size decreased as the MLSS concentrations increased. Carbohydrate fractions of both EPS and SMP contributed to fouling more than protein fractions. The impact of flux on fouling rate was small as long as the operating flux was less than critical flux, a trend found independent of MLSS concentration. Aeration velocity exhibited positive impacts on fouling control at all MLSS concentrations; however, the degree of this impact decreased significantly with increasing MLSS concentrations. Increasing MLSS concentration significantly decreased permeability values and increased fouling rates at each flux tested, a trend consistent for all aeration velocities. It was concluded that membrane fouling was affected by a combination of factors including operating flux (beyond the critical flux), MLSS concentration (thus the concentrations of both carbohydrate and protein fractions of EPS) and aeration intensity.