Introducing the European beaver to the catchment area, which adjusts the habitat to its own needs (by building dams), may have a positive impact on the ecology, geology, and hydromorphology of rivers and intensify the water self-purification process. In this study, a comparative assessment of the ecological status was made between the areas where the species Castor fiber L. occurs (habitat type A) and the areas unaffected by the influence (habitat type B). For this purpose, the Macrophyte River Index (MIR) and the Hydromorphological River Index (HIR) were calculated, along with the floristic indicators of biodiversity: species richness and Margalef, Shannon–Wiener, and Simpson indices. Only 35% of the sites met the standard of good ecological status. The presence of hypertrophic species and anthropogenic modifications of the river bed had a negative impact. The spread of beavers has a significant positive effect on changes in hydromorphological conditions and water levels in the river. The water levels in habitat types A and B were 0.504 and 0.253 m, respectively. There were statistically significant differences in the HIR values between habitat types A and B, which were 0.585 and 0.535, respectively. In habitats of type A, the heterogeneity of the current and bed material as well as the diversity of elements accompanying the tree stands increased. Research has shown greater species richness and greater biodiversity of macrophytes in the habitats of beaver dams. The research confirmed the significant influence of the European beaver on changes in the environment. The activity of beavers intensifies the processes of introducing wetland and rush species to forest areas.