A calibrated model of the patent-pending integrated biohydrogen reactor clarifier system (IBRCS) using BioWin was used to evaluate the impact of sludge and/or feedstock pre-treatment for methanogens inhibition in a dynamic simulation for 90 days with and without methanogens suppression. Dynamic simulations at four different OLRs ranging from 6.5 to 103 gCOD/L-d have shown that without any pre-treatment, the system was capable of washing out methanogens and enriching hydrogen producers. The average methane gas content in the reactor's headspace was 4% after 7 days of continuous operation, decreasing sharply to less than 0.5%, while the maximum reduction in hydrogen gas was <10%. The hydrogen gas content in the headspace ranged from 65% to 72%. Simulating the impact of extended SRT ranging from 3 days to 20 days on the performance of the IBRCS revealed that up to an SRT of 5 days hydrogen production was predominant with a reasonable deterioration in the production rate by 20%. Biomass distribution showed that at SRTs up to 20 days, acetoclastic methanogens were naturally eliminated. However, hydrogenotrophic methanogens had a significant impact on the overall hydrogen production rate where most of the hydrogen gas produced was consumed at SRTs of 10 days and 20 days. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.