Since a certain level of hydrodynamic shear force is needed in the formation of microbial granules for wastewater treatment, a method for quantifying the shear stresses in a microbial granular sludge reactor is highly desirable. In this work a novel energy-dissipation-based model was established and validated to quantitatively describe the shear stresses in a granular sludge sequencing batch reactor (SBR). With this model, the shear stress at the solid–liquid interface in an SBR was estimated and the relative magnitudes of shear stresses induced by fluid, gas bubble and collision on granules were evaluated. The results demonstrate that the effect of reactor geometry on the global shear stress was significant. Both the shear stress at the microbial granule surface and the biomass-loss rate increased with an increase in biomass concentration in the SBR. The gas bubble and the collision were found to be the main source for the shear stress at the granule surface.