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This paper reports the results of an experimental study specifically aimed at developing a simple methodology for calculating hydrodynamic shear forces in a sequencing batch biofilm reactor (SBBR) system with granular biomass. Using such a methodology, the hydrodynamic shear forces are simply calculated by measuring bed porosity and pressure losses. In addition, by applying this methodology an explanation for the biomass evolution from biofilm to granules under aerobic conditions has been provided and the following mechanism has been proposed: (i) formation of a thin biofilm that fully covers the carrier; (ii) increase of biofilm thickness; (iii) break-up of the attached biofilm with release of biofilm particles; (iv) rearrangement of biofilm particles in smooth granules. The hydrodynamic shear forces trend during the start-up period provides an explanatory key for the generation process of granular biomass. In fact, during the first two steps, the SBBR is characterized by rather weak shear forces values (lower than 1 dyn/cm2). Under these weak shear forces, the biofilm grows by increasing its thickness through a porous structure and weak adhesion strengths. Such a continuous increase of biofilm thickness produces an increase of the shear forces with negative effect on biomass stability, causing the detachment of biofilm particles. In turn, such detachment causes a further sharp increase of shear forces (more than 10 times) that promotes the rearrangement of the detached biofilm particles in smooth granules. A correlation between biomass density and hydrodynamic shear forces was observed. In particular, the biomass density linearly increases with the increase of shear stress.