The present study aims to extend the systematic knowledge on the quantitative and qualitative composition of the aquatic microbiome in large and economically significant Bulgarian reservoirs. Water samples were collected within 4 monitoring campaigns from 9 reservoirs, belonging to 4 national types of standing water bodies. Analyses include physiological profiling (CLPP) and next generation sequencing (NGS) of the V3-V4 hypervariable region of 16S rRNA gene. The surveyed water bodies can be divided into three groups based on their AWCD (average well color development) and specific activity. The communities in Koprinka, Ovcharitsa, Aheloy and Ivaylovgrad showed high steepness of the kinetic curve rapidly reaching a plateau. AWCD indicates that these communities are dominated by a limited number of fast-growing p-strategists. The second group include Dospat and Ogosta, while Studen Kladenetz, Alexander Stamboliyski and Zhrebchevo were consolidated in a separate group with greater biodiversity and conditions suitable for the development of slow-growing k-strategists. The NGS generated 5420 operational taxonomic units (OTUs), affiliated to 1066 genera. The analysis of the taxonomic composition and the abundance showed that communities are formed by similar dominant complex, with > 95% of the total number of sequences affiliated to representatives of only 10 phyla including Proteobacteria, Actinobacteria, Cyanobacteria, Verrucomicrobia, Firmicutes, Acidobacteria, Chloroflexi, Gemmatimonadetes and Fusobacteria in decreasing order. The communities differ mainly in OTUs forming a minor component based on their relative abundance. Cluster analysis of the genera distribution along the longitudinal axis of the water bodies revealed that positioning of net-cage aquaculture farms leads to an increase of the abundance of Cyanobacteria and Bacteroidetes. The second cluster groups the sites located at the walls of water bodies. The river inflow sites and the open aquatory are characterized by a similar composition. CLPP and NGS analysis revealed that water bodies are characterized by good self-purification ability, despite the presence of net-cage farms.