Despite significant progress in recent years, understanding the rules governing the assembly of natural communities is still challenging and knowledge of how the integration of nonnative species may disrupt community structure and function is needed. To address this challenge, we collated stable isotope data for 159 freshwater fish communities around the world with and without nonnative species and quantified spatial variation in both community isotopic functional diversity and intraspecific variation in species niches. Using a null model and partial least squares path analysis, we then evaluated how the interplay between abiotic (historical, energetic, climatic, habitat size) and biotic (niche segregation) factors shape community structure and functional diversity, and how these relationships have changed, and with what consequences, in the presence of nonnative species. We found that niche partitioning is a primary force underlying the structure and functional redundancy of native fish communities, which may be governed by a synergism between contemporary climate, productivity and habitat size. We also found evidence of a legacy of historical climate on functional diversity, independent from species richness. By contrast, path models of communities containing nonnative species demonstrated lower explanatory power and had no clear association with any of the abiotic or biotic factors. In conclusion, we demonstrated that strong spatial patterns in community structure and functional diversity of freshwater fish communities exist at the global scale, underlined by the complex interplay between external and internal filters, but that these patterns may be blurred by anthropogenic species introductions. Our results further highlighted the importance of accounting for realized species niches and species status (i.e., native and nonnative) when investigating questions related to the assembly and functional diversity of multitrophic communities.