Andean river ecosystems in South-central Chile possess a unique biogeography with high levels of endemism and challenge increasing pressures associated with habitat fragmentation and biological invasions. This doctoral thesis evaluates ecosystem resilience potential, understood as the capacity of a system to resist and maintain its functional integrity, in the Biobío and Imperial river basins. The "Three Rs" conceptual framework (Resources, Recruitment, and Refugia) was employed as a diagnostic tool for resilience potential, integrating geomorphological hierarchy with host–parasite interaction ecology. Under this holistic perspective, results demonstrate that fluvial geomorphology is a fundamental determinant of biotic architecture. The first chapter, conducted in the Biobío basin, analyzed the influence of Functional Process Zones (FPZs), which correspond to large river segments with similar geological and morphological histories that occur repeatedly and discontinuously along the longitudinal dimension of the river. These findings revealed that physical complexity in complex reaches, such as braided rivers, promotes interaction networks with higher modularity, strengthening ecological resistance by limiting the spread of perturbations within the network. The second chapter compares the Biobío and Imperial basins to evaluate taxonomic and functional metrics that contribute to ecosystem resilience. These results indicate that Strahler order, a hierarchical system that classifies channels based on the number and arrangement of tributary confluences, where headwaters are designated as first order, was a more sensitive resilience predictor than FPZs, particularly for parasite assemblages. In contrast, the Biobío basin exhibited significant deficits in the recruitment mechanism due to the loss of hydrological connectivity caused by the presence of dams. The third chapter focuses on a press or persistent disturbance, specifically biological invasions by salmonids and poeciliids. These invasions reconfigure transmission networks, reducing richness and simplifying interaction architecture through transmission interference and spillback, where the introduced species successfully integrate into the life cycle of local parasites. It is concluded that metazoan parasites are more sensitive bioindicators than their hosts and that integrating longitudinal connectivity (Strahler order) with local geomorphological heterogeneity (FPZs) allows for identifying stability hotspots more effectively. These patterns highlight that maintaining connectivity and functional redundancy is essential to protect the ecological stability of Andean rivers.