The activity and growth of microorganisms for renewable energy production are still influenced by the dead zones created in bioreactors. These areas form a nutrient and thermal gradient, causing an abundance of food in certain areas compared to famines in other areas of same bioreactor. The current study is a step in identifying those dead zones, followed by another step in improving the flow of media inside the reactor. The results indicated that the inner parts of the bioreactor may be a crucial factor in the creation and spread of such dead zones. For example, the position of the disc-type diffuser contributes to the generation of those areas at the bottom of the reactor. It was inferred from the fluid movement in reactors using the annular-type diffuser proposed in the current study. The bubble size, gas mass flux, and radiuses of fillet, as the most important factors, were examined in both bioreactors. The results revealed a noticeable improvement in these parameters in this area of the reactor when the disc diffuser was replaced by the annular diffuser. For example, the average liquid velocity was recorded in the lower part of the modernized reactor at 0.0198 m/s, while the velocity was recorded in the conventional reactor at 0.00077 m/s under same bubbles diameter used in both reactors (0.125 mm). The inclusion of the effect of the presence of microorganisms in mathematical models was also addressed in the current study. The results showed that the amount of oxygen remaining at the bottom of the reactor after bio-consumption in the presence of the annular diffuser was higher than that in the conventional reactor. This clearly emphasizes the importance of the design of the internal parts of the bioreactor.