This study investigates the distribution of shear stress in a lab-scale membrane bioreactor consisting of a 56 mm-diameter cylindrical test cell, a 0.25 mm-thick polyethersulfone membrane, and a centrally mounted 35 mm rotating impeller. Computational Fluid Dynamics (CFD) simulations were used to examine how impeller speed and geometry affect wall shear stress across the membrane surface. Higher rotational speeds significantly increased shear stress, with the highest levels observed near the impeller rim and a marked decline beyond a radial distance of 0.0175 m due to wall-induced flow dampening. To validate CFD predictions, Optical Coherence Tomography (OCT) was employed for in-situ, real-time biofilm monitoring. OCT results confirmed that low-shear regions—particularly at the membrane periphery—were more prone to rapid and extensive biofilm accumulation, whereas high-shear areas exhibited delayed or reduced fouling. To improve shear distribution and minimize localized fouling, a multi-objective optimization was performed using response surface methodology. This led to an enhanced impeller design that promoted more uniform and effective shear coverage across the membrane. The integration of CFD modeling, experimental validation, and optimization provides a robust framework for the design of membrane systems with improved anti-fouling performance and operational stability.