A methodology is proposed for the model calibration of nutrient-removing laboratory-scale SBRs under limited aeration. Based on in-process measurements and influent wastewater characterization, the ASM2d model was modified by adding an organic nitrogen module incorporating a hydrolysis mechanism. After calibration, the simulation results showed that enhanced biological nutrient removal occurred during the fill period and under reduced aeration achieving so-called 'simultaneous nutrient removal'. A model-based systems analysis was performed in terms of the contributions of different processes to overall oxygen, nitrogen and phosphate utilization. In each phase, simultaneously occurring biological reactions were compared using the calibrated model. According to the calibrated model, 61% of all denitrified nitrate is denitrified during the mixing/filling phase. On the other hand, 17% of all denitrified nitrate is consumed by simultaneous nitrification-denitrification during the first aerobic period. The aerobic and anoxic P-removals were quantified as 73% and 12%, respectively. (c) 2006 Society of Chemical Industry.