The main objective of this paper is to evaluate the effect of filamentous bulking sludge on the predicted performance of simulated plant-wide WWTP control strategies. First, as a reference case, several control strategies are implemented, simulated and evaluated using the IWA Benchmark Simulation Model No. 2 (BSM2). In a second series of simulations the parameters of the secondary settler model in the BSM2 are automatically changed on the basis of an on-line calculated risk of filamentous bulking, in order to mimic the effect of growth of filamentous bacteria in the plant. The results are presented using multivariate analysis. Including the effects of filamentous bulking in the simulation model gives a-more realistic-deterioration of the plant performance during periods when the conditions for development of filamentous bulking sludge are favourable: compared to the reference case where bulking effects are not considered. Thus, there is a decrease of the overall settling velocity, an accumulation of the total suspended solids (TSS) in the middle layers of the settler with a consequent reduction of their degree of compaction in the bottom. As a consequence there is a lower TSS concentration in both return and waste flow, less biomass in the bioreactors and a reduction of the TSS removal efficiency. The control alternatives using a TSS controller substantially increase the food to microorganisms (F/M) ratio in the bioreactor, thereby reducing both risk and effects of bulking sludge. The effects of ammonium (NH(4)(+)), nitrate (NO(3)(-)) and reject water control strategies are rather poor when it comes to handling solids separation problems.