Biological invasions have a negative impact on ecological interactions, such as competition and predation. The ecological impacts on native communities may also affect the environmental and spatial processes that are important in determining community structures. Here, we investigated the effects of invasive species composition on the native community and the processes that determine it using lake fish species compositions estimated via environmental DNA metabarcoding. The results of PERMANOVA analysis showed that native fish assemblage patterns changed significantly along with the composition of invasive species. Furthermore, we observed that the diversity of invasive species acted as a potent ecological filter, driving native fish communities towards biological homogenization. Distance-based redundancy analysis revealed that invasive species alter the relationship between ecological communities and their environment. This study suggests that invasive species may obscure distinct environmental signals by having broader environmental tolerances than native species. When comparing the relative importance of environmental factors and spatial structure in determining species composition, it was found that fish species composition in lakes is more strongly influenced by environmental factors than spatial structure. However, the predictive power of these factors varies with the presence of invasive species, being most evident in native-only communities. Our results suggest the need to understand the impact of invasive species on native species, not only through direct effects, but also through the complex effects involving the diversity level of invasive species.