Bulking sludge problems are commonly reported in biological nutrient removal (BNR) systems. This has led to the general belief that intrinsic BNR conditions favor the growth of undesirable and excessive filamentous bacteria. The present study shows that other factors have a major role in bulking, and not the BNR conditions. These factors have been verified in well-controlled, strictly anoxic-aerobic and strictly anaerobic-aerobic sequencing batch reactor systems. The experimental results show that conditions known to be responsible for bulking sludge in aerobic systems (i.e., low concentration of electron donor and/or electron acceptor) did not lead to bulking. Even when acetate was present at very low concentrations in the aerobic stage of an anaerobic-aerobic bio-P system, the sludge settleability remained very good. This clearly demonstrates that good bio-P activity can stabilize and improve sludge settleability. The presence of microaerophilic conditions in the anoxic stage of the anoxic-aerobic system was the only factor leading to worsening sludge settling characteristics. The results are discussed in light of our previous hypothesis about the importance of diffusion-limited substrate uptake for the development of filamentous structures in biological flocs. The hypothesis is extended to anaerobic-aerobic and anoxic-aerobic conditions, typical of BNR-activated sludge systems. Taking into account the effect of feeding patterns on biochemical rates and on the development of filamentous bacterial structures, we recommend the adoption of plug-flow selector configurations, with strictly anaerobic and/or strictly anoxic conditions, wherein microaerophilic conditions are excluded, in order to maintain reliable and robust BNR performance. (C) 2004 Wiley Periodicals, Inc.