Regime supervision over a condition of microbial plankton in the last five years (2008-2012) confirm the natural recurrence of development of microbial communities, both within a year, and in interannual aspect. Activity of microorganisms in Baikal submits to rigid regulation of trophic and parametrical factors of an ecosystem. On the total number of microorganisms, the vertical zonal distribution, especially during the periods of temperature stagnation of water masses is shown. The microbial oligotrophic complex of the Baikal waters in an euphoric zone of the lake (on the average a layer of 0-100 m) functions in strict accordance with rhythmics of development of primary producers of an ecosystem - planktonic algae.