Capillary electrophoresis (CE) is presented as a technique for the separation of polystyrene nanoparticles (NPs, particle diameters ranging from 30 to 300 nm) through a bare fused silica capillary and ultraviolet detection. The proposed strategy was also assessed for other types of nanoplastics, finding that stronger alkaline conditions, with an ammonium hydroxide buffer (7.5%, pH = 11.9), enabled the separation of poly(methyl methacrylate), polypropylene, and polyethylene NP for the first time by means of CE for particle diameters below 200 nm. Particle behavior has been investigated in terms of its effective electrophoretic mobility, showing an increasing absolute value of effective electrophoretic mobility from the smaller to the larger sizes. On the other hand, the absolute value of surface charge density decreased with increasing size of NPs. It was demonstrated and quantified that the separation mechanism was a combination of linear and nonlinear electrophoretic effects. This work is the first report on the quantification of nonlinear electrophoretic effects on nanoplastic particles in a CE system.