The efficiency of slug flow for fouling control of flat sheet (FS) membrane bioreactors (MBRs) is hindered by uneven bubble distribution leading to inhomogeneous shear stress profile on the membrane. In this work, a 3D CFD model was developed enabling prediction of the hydraulic performance of a novel aeration system designed to reduce the uneven bubble distribution in a full-scale FS MBR. Bubbles generated with aeration channel submerged in 8.0 g/L activated sludge were found to be unevenly distributed with up to 12 folds difference in gas mass flow per single nozzle. More than 41% higher gas mass flow was obtained at nozzles located at higher heights compared to lower nozzles at aeration intensities ranging from 12 m(3)/h to 20 m(3)/h. The subsequent uneven bubble distribution in membrane modules contributed to uneven shear stress distribution resulting in uneven fouling performance of the membrane module. Locating the aerator at a mediate distance of 20 cm to the membrane module (in the range of 15 cm to 25 cm) resulted in higher shear stress at locations closer to the permeate collector where higher flux occurred with a maximum 2.4 times increase in average shear stress. The CFD model was validated by comparison of the simulated height of the air column and bubble frequency with experimentally measured data obtained using a high-speed camera.