Coastal lagoons, characterized by their rich biodiversity and productivity, play a vital role in ecosystem services such as climate regulation, food production, etc. Since they have limited water exchanges and long hydraulic retention times, they are ecosystems highly vulnerable to anthropogenic factors and the accumulation of pollutants. In this study, we aimed to investigate the impact of Hydrogen Sulphur (H₂S) concentration and salinity infusion on the community diversities of bacteria, phytoplankton and zooplankton of a hypereutrophic coastal lagoon, Küçükçekmece Lagoon, located in Istanbul (Türkiye). Surface water samples were collected from three sites, along with samples from various depths (surface, 9 m and 18 m) throughout the water column in June 2022. The bacterial community structures were assessed by 16S rRNA gene-targeted sequencing using MinION (ONT), and phytoplankton and zooplankton diversities were analysed by microscopy. The results showed that the communities in the surface waters and the middle layer of the lagoon were quite similar. However, there was a clear shift in the community structure of the samples collected from the deepest part (18 m), which was under anoxic and high salinity conditions. The bacterial community was predominated by Sulfurimonas (15%), Sulfurovum (7%), and Draconibacterium, (7%) which can be related to the anoxic conditions and high H₂S concentration (20.39 mg/L). The results revealed that the responses of phytoplankton and zooplankton communities to the salinity increase were significant. Dominant phytoplankton, Cylindrotheca closterium, and dominant zooplankton, Acartia clausii, found in the deeper layer with high salinity are generally known as indicators of marine pollution. Although there were historical data on physicochemical properties and zooplankton and phytoplankton community diversities in this lagoon, this research provides the first extensive examination of such community structures, including the bacterial community of this lagoon, and lays the groundwork for future research in this aquatic ecosystem.