Membrane Bioreactors (MBRs) have been used successfully in aerobic biological wastewater treatment to solve the perennial problem of effective solids-liquid separation. The optimisation of MBRs requires knowledge of the membrane fouling, mixing and biokinetics. MBRs are designed mainly based on the biokinetic and membrane fouling considerations even though the hydrodynamics within an MBR system is of critical importance to the performance of the system. Consequently, the effect of the flow regime in the MBR process unit has been an insufficiently understood aspect of MBR design. Current methods of design for a desired flow regime within the MBR are largely based on empirical techniques (e.g. specific mixing energy). It is difficult to predict how vessel design in large scale installations (e.g. size and position of inlets, baffles or membrane orientation) affects hydrodynamics, hence overall performance. Computational Fluid Dynamics (CFD) provides a method for prediction of how vessel features affect the hydrodynamics and thus optimise MBR design and performance. In this study, a CFD model was developed which accounts for aeration and membrane configuration. As expected, aeration was found to be the main mixing mechanism. It was also discovered, with comparison to a previous modelling study [1], that inlet position may not greatly influence internal recirculation but can bring system closer to complete mixing, prevent 'short circuiting' and reduce 'dead zones'.