To model biological nitrogen and phosphorus removal systems with an affordable complexity, the ASM2d model structure is based on many assumptions. In this study, some of these assumptions, however, were observed to become invalid when the biological behaviour in the system altered in response to changes in the operation of the system, a pilot-scale N and P removing SBR. Particularly, the three applied operational scenarios resulted in three distinctive responses in the SBIR, namely pronounced limitation of the hydrolysis of the organic nitrogen, nitrite build-up during aerobic conditions and also nitrite build-up during anoxic conditions. This shows that even for the same system with the same influent wastewater composition, the model structure of the ASM2d does not remain constant but adapts parallel to dynamic changes in the activated sludge community. On the other hand, the three calibrated ASM2d models still,lacked the ability to entirely describe the observed dynamics particularly those dealing with the phosphorus dynamics and hydrolysis. Understanding the underlying reasons of this discrepancy is a challenging task, which is expected to improve the modelling of bio-P removing activated sludge systems.