A modified Discrete Element Method incorporating force models for calculating van der Waals forces, electrostatic repulsion forces, hydrodynamic lubrication forces, magnetic dipole-dipole interactions and Brownian effects was applied towards the study of shear aggregation of non-magnetic and magnetic colloidal nanoparticles. The effects of initial solid volume fraction of nanoparticles, initial morphology of aggregates formed via self-assembly in the absence of fluid flow and shear rate when simple shear flow was applied were investigated. The time evolution of the various forces present within these systems was analyzed to provide a more fundamental and mechanistic understanding of the various phenomena observed during shear aggregation of the non-magnetic and magnetic colloidal nanoparticles.