The biological variety of aquatic ecosystems is significantly impacted by the chemical and microbiological composition of water bodies, and there is strong reciprocal feedback between these two factors, especially for reservoirs, which can and do have a significant impact on neighboring ecosystems. Today there is an acute need to identify the most effective and economically feasible methods for cleaning and restoring water bodies. Therefore, the aim of the study was to find strains of microorganisms which are capable of biodegrading such problematic pollutants as insoluble phosphates and excess nitrogenous compounds and at the same time, are capable of suppressing the bacterial composition in reservoir waters. In the course of the research, a number of the most active strains of microorganisms were isolated from lake water samples. Five isolates were obtained from salt water and the isolates were then identified using morphological, and biochemical techniques, as well as the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In addition to the characterization and identification of the isolates, the species-specific levels of phosphate solubilizing, and nitrifying activities were also established. Thus, all isolated strains were studied and characterized, and their influence on the content of minerals such as phosphorus and nitrogen, which are important for living organisms in water, was studied. In summary, the Pseudomonas Extrem-Orientalis isolate was observed to be highly effective in solubilizing phosphates, nitrifying, and had the greatest antagonistic capacity among the investigated isolates. The information gleaned from the study’s findings helps raise more awareness in the field of microbiology and water treatment in general. The findings offer promise for the development of biopreparations with bioremediation capabilities for cleaning polluted water bodies of pollutants from various sources.