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In this paper, we consider the development of reliable tools to assess the water quality and state of aquatic ecosystems in dynamic conditions a crucial need to address. One of such tools could be devised by monitoring the taxonomic structure of reservoirs’ microbiomes. Microbial taxa’s ecological and metabolic characteristics suggest their essential roles in maintaining the water ecosystem’s environmental equilibrium. The study aimed to explainthe role of diversity and seasonal variability of the microbial communities in the ecosystem stability on the example of Goczałkowice Reservoir (Poland). The structure of the reservoir microbiome was studied using bioinformatics and modeling techniques. Water was sampled periodically in July & November 2010, and April 2011 at four representative sites. The abundance and relative fraction of the limnetic taxonomic units were determined in respectto the physicochemical indices. Significant seasonal variations in the number of operational taxonomic units (OTU)were observed within the reservoir basin’s main body but not at the main tributary’s mouth. The highest valuesof the correlation coefficients between OTU and physicochemical variables were obtained for Burkholderiales,Pseudoanabenales, Rickettsiales, Roseiflexales, Methylophilales, Actinomycetales, and Cryptophyta. Thesemicroorganisms are proposed as indicators of environmental conditions and water quality. Metataxonomic analyses of the fresh water microbiome in the reservoir, showed that microorganisms constitute conservative communities that undergo seasonal and local changes regarding the relative participation of the identified taxa. Therefore, we propose that monitoring those variations could provide a reliable measure of the state of aquatic ecosystems.