Upwelling water generally transports abundant nutrients to fertilize the euphotic zone and promotes larger phytoplankton to thrive. In contrast, knowledge about the composition of prokaryotic picoplankton associated with the scale of upwelling is limited. In this study, the population compositions of prokaryotic picoplankton, with particular focus on Synechococcus, under two diverse hydrographic conditions in the shelf-margin upwelling system were compared in detail. During the study period of 2009, an upwelling event was observed. In contrast to conventional upwelled water, the surface of this upwelling was covered with a thin layer of nutrient-depleted water. Although the water exchange created a low-nutrient stock environment, which fell below traditional chemical detection limits, its flux was likely sufficient to support the growth of the Synechococcus clade-II lineage. In comparison with the hydrography in 2009, no obvious upwelling occurred, and oligotrophic water primarily occupied the upper layer during the study period of 2010. The abundance of Synechococcus significantly declined to approximately half its numbers observed in 2009. While the Synechococcus clade-II were still the predominant population, their proportion in the 16S rRNA gene library decreased to approximately 50%. The remaining part was replaced with α-Proteobacteria and various heterotrophic bacteria. The results of the present study, combined with those obtained in previous studies, yield a more comprehensive understanding of the phytoplankton community dynamics in this varied ecosystem.