This paper illustrates the method to predict the production of biohydrogen and biogas from the horizontal and vertical continuous mixed tank reactor using a numerical approach. Utilization of computational fluid dynamics on the estimation of bioreactor performance is very crucial owing to the uncertainty in the numerical results. Since there has been little work on CFD to determine the influence of hydraulic retention time, impeller speeds, vortex growth, and pH on biohydrogen yield rate the effort had been made. A series of simulations are done with optimal boundary conditions to ensure maximum hydrogen and biogas production rate. Two types of reactors HCSTR and VCSTR are operated at different impeller speed from 40 rpm to 120 rpm. Further, the rate of HRT and organic loading are varied. As the rpm of the impeller increase the rate of hydrogen and biomass production increases not later than 80 rpm. Meanwhile, the optimal range of HRT and pH are 4–8 h and 6.0–8.0. Running the impeller at optimized rate with derived conditions leads to high hydrogen and biogas production of 6 LH2/Ld and 30 L/d. The obtained results are validated with the experimental findings to compare the uncertainty formed due to the numerical simulations. The optimum boundary condition obtained from the study is expected to provide the essential knowledge in establishing the full-scaled reactors.