Freshwater ecosystems appear more vulnerable to biodiversity loss due to several anthropogenic disturbances and freshwater fish are particularly vulnerable to these impacts. We aimed to (1) identify the contribution of land use, spatial variables, and invasion degree in determining freshwater fish alpha (i.e., species richness) and beta (i.e., local contributions to beta diversity, LCBD) diversity, evaluating also the relationship between invasion degree and nestedness (β$$ \beta $$nes) and turnover (β$$ \beta $$sim) components of beta diversity. (2) Investigate the relationship between alpha diversity and LCBD, under the hypothesis that alpha diversity and LCBD correlate negatively and (3) investigate the relationship between species contributions to beta diversity (SCBD) and species occurrence, hypothesizing that non‐native species show a lower contribution to beta diversity. The linear mixed models and the partition of R2 retained the invasion degree as the most important variables explaining alpha and beta diversity, having a positive relationship with both diversity components. Furthermore, land use related to human impacts had a positive influence on alpha diversity, whereas it showed a negative effect on LCBD. Regression model further showed that invasion degree related positively with β$$ \beta $$sim, but negatively with β$$ \beta $$nes, suggesting that non‐native species were involved in the replacement of native species in the fish community. Alpha diversity and LCBD showed a weak positive correlation, meaning that sites with low species richness have higher LCBD. SCBD scaled positively with species occurrence highlighting that rarer species contribute less to SCBD. Finally, native and exotic species contributed similarly to beta diversity. These results suggest that invasion degree plays a central role in shaping alpha and beta diversity in stream fish, more than land use features reflecting habitat alteration or other geospatial variables. Furthermore, it is important to evaluate separately the native and the non‐native components of biotic communities to identify linkages between invasion dynamics and biodiversity loss.