The fate and effect of the antimicrobial compounds benzalkonium chlorides (BACs) on the biological nitrogen removal (BNR) processes for a continuous-flow, three-stage laboratory-scale BNR system were modeled. Three kinetic sub-models, corresponding to each reactor, were developed and then combined in a comprehensive ASM1-based model. Kinetic parameters for the three sub-models were evaluated using experimental data obtained from independent batch assays. The biodegradation of BACs was modeled with a mixed-substrate Monod equation. The inhibitory effect of BACs on the utilization of degradable COD and denitrification was modeled as competitive inhibition, whereas non-competitive inhibition was used to model the effect of BACs on nitrification and inhibition coefficients were evaluated. The model simulated well the long-term performance of the BNR system treating a poultry processing waste-water with and without BACs. Enhanced BAC degradation by heterotrophs and increased resistance of nitrifiers to BACs, reflecting acclimation/enrichment over time, is a salient feature of the model. (C) 2012 Elsevier Ltd. All rights reserved.