Submarine wastewater discharges are considered an important source of microbiological and chemical pollution in the coastal zone, directly affecting microbial biodiversity. In this study, the effects of effluent intrusion on the surface and bottom microbiome of the water column were analyzed over a 5-month period. The density of the water column was assessed to obtain the stratification status of the water column. In addition, Brunt-Väisälä frequency and potential energy anomaly were used to investigate the density stratification strength and water column stability. Regardless of the stratification status, different phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) are found at the bottom and surface of the water column, reflecting the human gut microbiome. In addition, several pathogenic genera were found at all sampling sites, including Acinetobacter, Arcobacter, Bacteroides, Escherichia-Shigella, Klebsiella, Pseudomonas, and Salmonella. Nutrients, in particular, were the driving factors for the changes in microbial communities. Therefore, a co-occurrence network analysis was conducted to explore the relationship between environmental factors and selected microbial taxa. Despite stratified conditions during most sampling campaigns, the effluent plume influenced the surface microbial community by introducing allochthonous bacteria. Taxonomic profiling of the microbial community, together with analysis of water column stability, provides a useful dataset for further studies of water quality deterioration in the coastal zone. In this respect, this approach provides an important framework for the development of a more effective and reliable wastewater treatment strategy.