Nanotechnology that is vigorously developed nowadays will inevitably let nanoparticles into water resources. Since these ultrasmall particles may have potential risks for human and animals, it is reasonable to consider urgently how to manage these polluted waters. The direct separation would be difficult due to their small size and high surface area, so AlCl3 is added to modify surface physicochemical properities of nanosilica in order to produce aggregates. Early stages and long time equilibrium of nanosilica aggregation are explored. In the kinetics study (early stage), the influences of particle concentrations and particle sizes are studied and compared. The aggregation results at long time equilibrium are further investigated, which shows the charge neutralization effect could be overcome by other mechanisms. More than 99% of the turbidity can be removed from aggregation of nanosilica by AlCl3 after sedimentation.