The effects of colloidal organic matter on nitrification and the composition of extracellular polymeric substances (EPS) in biofilms were studied in two parallel bench-scale biological aerated filters (BAFs) fed with different organic carbon sources. The study filter used starch and glucose to model colloidal and soluble organic carbon, respectively, while the control filter used glucose as the sole organic carbon source. Studies with different COD/NH4+ (C/N) ratios (0.5-6.0) showed that the increase in organic matter in the influent resulted in the displacement of nitrification from the bottom to the upper part of filter bed. It was observed that the greater reduction in nitrification was caused by colloidal organic matter rather than by soluble organics at the same COD concentration. The starch hydrolysis took place in the bottom 40cm of the filter bed, which implied that hydrolysis of colloidal organic matter into smaller molecules could not be the limiting step of its oxidation in the biofilm. In addition, biofilm surface morphology and EPS composition were subject to different substrate conditions. Polysaccharide was the primary and protein the minor component of the EPS extract. In the study filter, the protein content of EPS diminished from the bottom to the upper layer of the filter bed, which was strongly correlated to the hydrolysis of colloidal organic matter.