The study on Lake Alalay, an urban alkaline lake facing increasing pollution, focused on the impact of coagulation treatment on its water quality and microbiome. The findings revealed higher nutrient concentrations, specifically phosphate and ammonium, compared to the 2019 benchmark. The lake was found to be dominated by Proteobacteria, followed by Cyanobacteria, with Desulfobacterota thriving in areas with low dissolved oxygen. Arthrospira and Roseobacter, halo-alkali-tolerant photosynthetic bacterial genera, were detected at all sampling points. Local phosphate and oxygen concentration variations led to distinct microbial communities on the lake's surface. Despite these differences, long-term ex-situ studies on water treatment with iron chloride and poly-aluminum chloride reduced the relative abundance of Cyanobacteria, promoting the presence of Proteobacteria and Bacteroidota. However, the coagulants required higher quantities than those typically used in small shallow lakes to precipitate phosphate and improve water quality effectively. Furthermore, the large-scale assay of lake water treatment with coagulants failed to eliminate Vibrio and Acinetobacter multidrug-resistant bacteria. In conclusion, the study underscores the need to prevent the inflow of polluted water into Lake Alalay and implement effective measures to deal with the existing chemical and biological contamination.