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Analysis of long-term dynamics of the fish assemblage diversity of 70 large lakes and reservoirs of Russia and other countries of CIS shows, that the response of the community to the increase of load consists of two phases. Under the weak loads the population waves amplitude increases. With intensifying influence the structural and functional features of the fish community changes. It causes the consideration of the biodiversity dynamics as a complex stochastic process. Simple comparative analysis of the biodiversity indices in different spans can result in erroneous conclusions.