Complex analysis of heterotrophic microbial communities at different depth of Lake Arakhley during periods of early spring and summer stratification allowed establishing trophic stability and main role of dominant heterotrophs. It was shown that minor forms of heterotrophs were found in uncultivable stage and were not involved in metabolic cycles of water reservoir during transit from homothermy to stagnation. The spectrum of heterotrophic microorganisms-indicators for lake water quality estimation was determined by molecular-genetic analysis of microbial communities with primer sets of different taxonomic levels and cultivation on selective media.