The world is facing serious climate change caused in part by human consumption of fossil fuel. Therefore, developing a clean and environmentally friendly energy resource is necessary given the depletion of fossil fuels, the preservation of the earth's ecosystem and self-preservation of human life. Biological hydrogen production, using dark fermentation is being developed as a promising alternative and renewable energy source, using biomass feedstock. In this study, beverage wastewater and agricultural waste were examined as substrates for dark fermentation to produce clean biohydrogen energy. A reference model including all major process steps was computed using the Aspen Plus software program and model valuations were based on the data obtained in our lab and/or a pilot scale process unit. A beverage company in northern Taipei was the source of wastewater used in the production of biological hydrogen, whereby the use of our hydrogen producing system resulted in a maximum annual profit with an annual return rate of approximately 81% with a working volume of 100 m(3) from wastewater and 30% with a working volume of 400 m(3) from agricultural waste using local price evaluation and approximately 60% with working volume of 200 m(3) from wastewater and 39% with working volume of 300 m(3) from agricultural waste. The optimal sizes of the commercial biohydrogen fermenters of wastewater and agriculture waste were 52.51 and 300.57 m(3), respectively which were simulated by local price. These results were derived from the Aspen Plus simulation, proving it's economic feasibility. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.