The Andean river basins of central–southern Chile face multiple anthropogenic disturbances, including water extraction, hydropower, mining, and industrial discharges, which affect their ability to adapt to new disturbances. Disturbance intensity forms a gradient from high (Maipo, Rapel, Biobío, Maule) through medium (Mataquito, Itata) to low (Imperial, Toltén). This study evaluated resilience in these eight river basins based on fish assemblages, using taxonomic and functional trait indices within the framework of the three Rs of resilience: resources, recruitment, and refugia. Taxonomic indices captured changes in species richness, abundance, diversity, evenness, and beta diversity, while functional traits reflected the fish species characteristics promoting resilience. Statistical tests revealed significant differences in resilience indices among basins. Recruitment was the most impacted resilience mechanism, with beta diversity revealing effects from river fragmentation in the Maipo, Rapel, and Biobío basins. The resources mechanism was also affected, primarily by land-use changes and water pollution, leading to low species richness in the Maipo, Rapel, Mataquito, and Maule river basins. Interestingly, basins with medium disturbance levels showed high resilience, indicating adaptive responses to moderate impacts. This study emphasizes the importance of multiple indicators to assess ecosystem resilience and calls for integrated strategies to address the complex challenges impacting freshwater biodiversity.