Marine microbial communities are the crucial players in biogeochemical cycles and sensitive to the environmental changes. It is of great significance to explore the dynamics of microbial communities under complex environmental conditions. The Gouqi island located in the East China Sea (ECS) is an aquacultural zone of Mytilus coruscus with unique environments shaped by the Changjiang River freshwater and ECS saline water masses. We conducted long-term water sampling within this region to investigate the prokaryotic and phytoplanktonic community compositions, diversities, structures and potential interaction using 16S/18S rRNA metabarcoding and metatranscriptomic analyses. Besides, we also measured temperature, salinity, pH, and concentrations of dissolved oxygen, particulate organic matter, dissolved organic matter and nutrients in the same samples. By clarified environmental factors, we divided the overall timescale into two distinct nutritional states: a higher salinity, more oceanic state in autumn and winter, and a more eutrophic state in summer. We figured out the different patterns of the microbial communities which were influenced by salinity and N:P ratio significantly, with the preeminence of Flavobacteriales and SAR11, respectively. We also found the higher Shannon index and more similar community structure in oceanic conditions. Compositional stability showed that the phytoplanktonic community was more stable than the prokaryotic community in response to temporal changes. Using weighed gene co-occurrence network analysis (WGCNA), we detected the co-occurrence patterns of microbial communities, indicating recurrence and asynchrony between prokaryotic and phytoplanktonic communities. Meanwhile, potential interactions showed the temporal changes of relationships such as Dinophyceae-Flavobacteriales, Dinophyceae-Rhodobacterales and Syndiniales-Flavobacteriales, which were dominant in summer and decreased after then. But they exhibited distinct peaks at different time points of summer, suggesting the influence of biotic competition and niche partitioning.  The higher expression of genes related to motility, chemotaxis and phytoplankton-derived molecules metabolisms in summer, such as FliC, CheC and dmdA, revealed that prokaryotic community had higher demand and competitions to phytoplankton-derived molecules in summer. These findings provide a detailed insight into how environments shape microbial community structure and potential interactions in a typical subtropical region.

seasonal variation, prokaryotic community, phytoplanktonic community, WGCNA, phytoplankton-prokaryotes interactions, aquacultural zone, metatranscriptomes