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The optimisation of submerged hollow fibre MBRs was achieved through a series of numerical simulations ranging from meso-scale simulations of the membrane module and filtration zone, to micro-scale simulations of the inhomogeneous distribution of filtration flux, and the effects of fibre displacement on surface shear and flux. A meso-scale Computational Fluid Dynamics model, coupled with sludge rheology models to account for the behaviour of mixed liquor and porous media models to represent the resistance of membranes to the fluid field, was developed and used to estimate shear stress in the filtration zone of a 1250 L pilot scale membrane bioreactor. These simulations indicated that the addition of iron salts altered the rheology of activated sludge and reduced the uneven distribution of shear stress, particularly in the lower zone of the membrane module. For the filtration zone design, the highest shear stress was predicted to occur for vertically oriented membranes aligned in parallel with air diffuser nozzles generating 10 mm diameter bubbles constrained to travel in the filtration zone by solid baffles encasing the membrane module. Micro-scale CFD modelling of flux as a function of fibre length, diameter, permeate collection modes (bottom-out, top-out and two-end out) was conducted on a single hollow fibre membrane. Results suggested that the local flux at the bottom was 43.8% lower than that at the top for a 2 m long hollow fibre operated in a top-out permeation mode, indicating an uneven flux distribution along fibre length. This can be improved by increasing fibre diameter or using two-side out permeation mode. Pressure profiles from meso-scale models of two-phase (liquid-air) flow were imported to the micro-scale models to account for the impact of aeration on flux. Under aerated conditions, a more even flux distribution was observed for the fibre with a bottom-out permeate collection mode than the one operated with a top-out permeate collection mode with the ratio of flux at the base to flux at the outlet of 12.2% compared to 23.3%. Fibre movement induced membrane surface shear was evaluated with microscale Fluid Structure Interaction (FSI) modelling. Surface shear was found to be 130% high for a moving fibre compared with a fixed fibre under the same aeration intensity. The average shear stress on a moving fibre could be increased by decreasing the Young’s modulus (more flexible fibre), increasing the fibre looseness and using fibre with larger diameter. In addition, the average shear around a bundle of 7 fibres with high packing density (666 m2/m3) was found to be 3.6 times greater than the bundle with lower packing density (172 m2/m3) moved at identical amplitude and frequency.