The Neotropical region is an important reservoir of functional diversity of freshwater fish in the world. Recent studies have shown that functional and taxonomic diversity in this region has increased as a consequence of the introduction of exotic species. However, little is known about how this phenomenon has modified functional diversity at the watershed level. In the present study, we analyze the spatio-temporal changes of functional diversity in 22 watersheds of continental Chile, hypothesizing that the introduction of exotic species could have contributed to increasing and homogenizing the functional diversity within and among watersheds. Toward this purpose, we implemented measures of functional diversity (FRic), β-diversity (FDiv), turnover (Ftur), and nestedness (Fnes) in two compositional stages, which we call “historical” and “current”. The former considered the most probable composition of native species prior to European colonization, while the latter considered the current distribution of native and exotic species. For these two stages, we determined the changes in (FRic, FDiv, Ftur, and Fnes between pairs of watersheds, as well as the effect of geographic distance. Our results showed that, on average, FRic has increased its historical value by 156%; on the other hand, ΔFDiv and ΔFtur decreased significantly from its historical composition to current one (ΔFDiv = −7.4%; ΔFtur = −13.2%; both P < 0.05), while nestedness showed no significant changes (ΔFnes = −3.6%; P > 0.05). Finally, geographic distance between watersheds was negatively and significantly correlated with change in β-diversity and spatial turnover (r = −0.267; r = −0.410, respectively; both P < 0.05), while ΔFnes did not show a significant correlation with distance (r = 0.178; P > 0.05). These results indicate that exotic species (a) have increased functional diversity in local assemblages, because they display historically absent functional features; and (b) have promoted functional homogenization between assemblages, which is more intense between geographically more distant ones. These findings suggest that, due to their functional features, the presence of exotic species poses a probable risk for the functional stability of watersheds in continental Chile, and that it is necessary to implement conservation measures to protect this unique fish fauna.