An attempt is made to study and simulate agglomerate dispersion and deformation in a cavity flow, as a typical Three-dimensional flow field, using Stokesian Dynamics (SD) and Macroscopic Flow Analysis. The break up and deformation behavior of two different agglomerate structures, a loose agglomerate with fractal dimension FD = 1.8 and a dense one with FD = 2.6, is examined in different flow paths. The interparticle forces are calculated using Van Der Waals and Born forces. Results show that agglomerates with a dense structure break up through detachment, while ones with loose structure deform and break into fragments through rupture. It is also found that the rearrangement of particles in the agglomerate can postpone break up in flow fields where rotation occurs, since it can dissipate stress through rearrangements.