In this paper, retrospective analyses of long-term changes in the aquatic ecosystem of Ladoga, Onega, and Imandra lakes, situated within North-West Russia, are presented. At the beginning of the last century, the lakes were oligotrophic, freshwater and similar in origin in terms of the chemical composition of waters and aquatic fauna. Three stages were identified in this study: reference condition, intensive pollution and degradation, and decreasing pollution and revitalization. Similar changes in polluted bays were detected, for which a significant decrease in their oligotrophic nature, the dominance of eurybiont species, their biodiversity under toxic substances and nutrients, were noted. The lakes have been recolonized by northern species following pollution reduction over the past 20 years. There have been replacements in dominant complexes, an increase in the biodiversity of communities, with the emergence of more southern forms of introduced species. The path of ecosystem transformation during and after the anthropogenic stress compares with the regularities of ecosystem successions: from the natural state through the developmental stage to a more stable mature modification, with significantly different natural characteristics. A peculiarity of the newly formed ecosystems is the change in structure and the higher productivity of biological communities, explained by the stability of the newly formed biogeochemical nutrient cycles, as well as climate warming.