High hydraulic retention times are commonly used in bioreactors, as they provide greater contact time between substrate and biomass. These reactors also operate at low flow rates to minimize damage to the biomass due to shear stress and drag. However, a high flow rate provides greater mixing, and thus the optimal operation condition is difficult to estimate. In this study, the effect of different flow rates on the behaviour of the phases in an anaerobic sequencing batch bioreactor is evaluated numerically. Fluent 15 code was used, considering the two-phase, transient, and turbulent flow in a three-dimensional mesh. The turbulence, the drag of the biomass flocs to the recirculation system, and the shear stress in the remaining solids were evaluated. For the reactor evaluated in this study, the flow rate of 189.4 g/s was found to be the most suitable, not only for the operation of the reactor, but also to provide energy savings in the operation of the recirculation pump.