Reports of marine organisms ingesting microplastics—formed from large plastic litter drifting in the marine environment by mechanical forces such as waves and photochemical processes initiated by sunlight, particularly ultraviolet rays—are increasing. However, the degradation process from microplastics to nanoplastics that are easily consumed by plankton located in the lower part of the food chain is not clear. Therefore, 200 nm diameter polystyrene (PS) latex particles—nanoparticle tracking analysis (NTA) calibration particles—dispersed in ultrapure deionized water were subjected to three types of agitation: rotation mixing, shaking, and flowing in addition to standing without agitation, and the physical degradation caused by agitation for 1 week at room temperature (23 °C) was evaluated. The degradation of the particles into nanosized particles was assessed by particle size distribution measurement using NTA and shape observation using field emission scanning electron microscopy (FE-SEM). In addition, the ratio of particle aggregation during incubation was calculated from the number of particles present in the region exceeding the particle size distribution range of the monodisperse particles before agitation with respect to the total number of particles. A shape change to a particle size of 100 nm or less was observed for the rotating and flowing of samples, and the influence of aggregation was suppressed to within 21% of the total particles calculated by NTA at the maximum. These results show that chemically stable PS can be degraded from micro- to nanosize with simple agitation in ultrapure deionized water.