Quaternary ammonium compounds (QACs) are surface-active organic compounds common in industrial cleaner formulations widely used in various sanitation applications. While acting as effective pathogenic biocides, QACs lack selective toxicity and often have poor target specificity. As a result, adverse effects on biological processes and thus the performance of biological nutrient removal (BNR) systems may be encountered when QACs enter wastewater treatment plants (WWTPs). Because of these impacts, there is motivation to screen wastewater influents for QACs and for process engineers to consider the inhibition effects of QACs on process evaluation and design of BNR plants. This paper introduces a mathematical model to describe the fate of QACs in a WWTP via biodegradation and bio-adsorption, and the inhibitory effect of QACs on nitrifiers and ordinary heterotrophic organisms. The model was incorporated as an add-on model in BioWin 5.3 and simulations of experimental systems were used for comparison of model results to measured data reported in the literature. The model was found to accurately predict the bulk phase concentration of QAC and the inhibition of nitrification with QAC concentrations ≥2 mg/L. This work provides a preliminary framework for simulation of BNR plants receiving inhibitory substances in the influent.