Recently, the global scientific community has shown interest in studying pit lake ecosystems. This interest is driven by a number of factors, including the significant role of pit lakes in enhancing regional biodiversity and providing ecosystem services. The Irkutsk region contains a large number of pit lakes. This study compares aquatic organism groups and the hydrochemical and physicochemical parameters of two pit lakes in the Cheremkhovo district. Thus, using the example of two lakes, three stages of colonization of pit lakes by macrophytes and aquatic invertebrates can be identified. These stages differ in both the level of development and organization of macrophyte communities and aquatic invertebrate communities. The obtained data demonstrate that even under common geological and geographical conditions, the formation of hydrobiocenoses in pit lakes can occur according to different scenarios. The results of the study show that the presence of a forest on the site of a future pit lake contributes to stabilization, a reduction in acidity, and the formation of a fully functioning aquatic ecosystem within less than 40 years. At the same time, the nearby lake, around which vegetation is still sparse, has a low pH (3.05), and the most favorable conditions are created by thickets of moss (Warnstorfia exannulata).