The progressive degradation of aquatic ecosystems and ecohydrological role of rivers is one of the most important global environmental issues. The loss of the ability of rivers to self-purify waters due to the disturbances of river continuity cause a lack of biological life in parts of rivers or even in an entire river. The appearance of alien species in degraded aquatic environments is an increasingly common phenomenon and constitutes one of the threats to biodiversity. The aim of the study was to evaluate the possible impact of alien species Potamopyrgus antipodarum (Gray, 1843) and Gammarus tigrinus (Sexton, 1939) on native invertebrates as well as the influence of environmental factors on the occurrence benthos fauna including also alien species. The study conducted in industrial area, in the River Ruda (Poland), showed that at the sites at which the occurrence of the two alien species was observed, the density of native benthos and diversity decreased significantly. CCA analysis showed that non-native species occurred in fast water velocity and that their presence was associated with high values of conductivity, hardness, and a high chloride content. The arrival of new species from other geographical areas is one of the factors that influences the species balance in native aquatic fauna. The number of alien species in freshwater ecosystems probably will increase in the future as new aliens are moved outside of their native ranges.