Variations of picoplankton groups were investigated over a one-month period in Daya Bay and Sanya Bay, in the northern South China Sea. The two coastal regions exhibited different variation patterns in physicochemical parameters. Moreover, the diel variations of picoplankton groups were different between the two bays. The abundance of the picoplankton in Sanya Bay displayed a pronounced diel variation, while it was not significant in Daya Bay. In addition, some similar patterns of picoplankton abundance were discovered. In the two bays, virioplankton exhibited the smallest fluctuation range, whereas picocyanobacteria fluctuated most markedly. The fluctuation range of picoplankton groups was larger in spring tide than in neap tide, especially in Sanya Bay. Random forest model analysis demonstrated that the variation of picoplankton groups was attributed to physical and chemical factors in Sanya Bay and Daya Bay, respectively. Therefore, our findings suggest that virioplankton abundance can persist more stably in response to changing environmental conditions compared to bacterioplankton and picophytoplankton.