Bacterioplankton play an important role in the marine microbial loop, and have a critical impact on carbon, nitrogen, and phosphorus cycling processes as well as energy flow by mediating the transformation of dissolved organic matter (DOM). Coastal ecosystems are jointly regulated by land-sea-air and human activities at multiple scales. Marine meso- and fine-scale physical processes can strongly alter the physical and chemical properties of coastal waters at small spatial and temporal scales, which may have a series of important impacts on coastal bacterioplankton communities and their linkages with DOM. However, there is still a lack of systematic knowledge of how bacterioplankton communities respond to highly dynamic meso- and fine-scale physical processes. In this study, we selected the northern South China Sea (NSCS) and the Taiwan Strait (TS), which are significantly affected by physical processes, as the experimental sites, and focused on typical meso- and fine-scale physical processes, including river plume, coastal current front, and internal wave, with the help of physical, chemical, and biological field cruises, and the use of high-throughput sequencing and other technological means to synthesize and characterize the response of bacterioplankton community structure. Additionally, employing various mathematical and statistical methods, we revealed the relationships between bacterioplankton communities and DOM driven by meso- and fine-scale physical processes.