This paper demonstrates the possibilities of detecting changes in populations of animals, based on the analysis of their dynamic phase portrait. This method allowed us to clarify the periodization of the process of naturalization of the Black Sea sprat (Clupeonella cultriventris) in the Rybinsk Reservoir and in detail describe the changes in the main dynamic characteristics of the population. On the example of zander (Sander lucioperca) in Lake Vozhe, the state was observed in which intra-population mechanisms activate which slow the increase in population (distribution of individuals from regions with high density). Use of this method allowed us to describe the new stable state of the population of grayling (Thymallus thymallus), which it entered as a result of increase in sport fishing. The data on time of presence of a population in equilibrium state allowed us to correctly unify the materials used for the analysis of changes in its age group.