A Stokesian dynamics model is presented to predict suspension viscosity and microstructure for concentrated suspensions. The influence of electrostatic repulsive forces, London-van der Waals attractive forces, and boundary interactions on the degree of shear-thinning is reported. Three different mechanisms for shear-thinning are described and quantified. The degree of shear-thinning caused by Brownian motion is well predicted by using random and layered structures. Shear-thinning for repulsive forces between particles is caused by the "melting" or breakup of an ordered or semicrystalline configuration as the shear rate increases. For suspensions flocculated into a secondary minimum, shear-thinning is produced by breakup of particle aggregates as the hydrodynamic forces dominate the interparticle forces. At high concentrations, the dispersed and flocculated suspensions can form slip planes that reduce suspension viscosity. Rough walls increase the viscosity predictions by an order of magnitude and cause the shear thinning prediction to compare well with experimental results from the literature.