Despite recent developments in process-based modeling of treatment wetlands (TW), the dynamic response of horizontal flow (HF) aerated wetlands to interruptions of aeration has not yet been modeled. In this study, the dynamic response of organic carbon and nitrogen removal to interruptions of aeration in an HF aerated wetland was investigated using a recently-developed numerical process-based model. Model calibration and validation were achieved using previously obtained data from pilot-scale experiments. Setting initial concentrations for anaerobic bacteria to high values ( 35–70 mg L−1) and including ammonia sorption was important to simulate the treatment performance of the experimental wetland in transition phases when aeration was switched off and on again. Even though steady-state air flow rate impacted steady-state soluble chemical oxygen demand (CODs), ammonia nitrogen (NH4–N) and oxidized nitrogen (NOx–N) concentration length profiles, it did not substantially affect corresponding effluent concentrations during aeration interruption. When comparing simulated with experimental results, it is most likely that extending the model to include mass transfer through the biofilm will allow to better explain the underlying experiments and to increase simulation accuracy. This study provides insights into the dynamic behavior of HF aerated wetlands and discusses assumptions and limitations of the modeling approach.