The effect of lowering the pH of the acidification reactor on the overall performance of a two-stage anaerobic wastewater treatment system was determined both experimentally and through simulation of a dynamic structured model. The system operated at low pH was then subjected to a short-term step increase in feed concentration. The measured and the predicted dynamic responses of reactor variables to the shock load were evaluated. The result indicated that lowering the pH setpoint from 6.0 to 5.3 led to a reduction in the external alkali addition by 30% without any significant deterioration in the final effluent quality. The model prediction showed good agreement with the experimental results for most reactor variables. The dynamic response of the system to a concentration shock load indicated a decrease in effluent quality during the disturbance, but the system did recover quickly as soon as the shock load terminated. The comparison between the experimental and the simulation results demonstrated the feasibility of the model to be applied for reactor design and operational evaluation purposes.