<p>Rivers are complex ecosystems that integrate three interacting domains, geomorphology, hydrology, and ecology, each hierarchically structured. This study aimed to assess links between river geomorphology and host–parasite interactions. Specifically, we examined the structure of parasite assemblages in fish and lamprey hosts in Functional Process Zones (FPZs), which are discrete geomorphic units distributed in patch-like patterns along river corridors, with contrasting geomorphic structure in the Biobío River basin, Chile. We assessed fish and lamprey assemblages, their parasites, and the structure of host–parasite networks across three rivers and three FPZs of varying geomorphic complexity. Analyses revealed significant differences in host and parasite assemblage composition among rivers and FPZs, with host assemblage structure driven by geomorphological gradients and parasite structure influenced by host habitat use and environmental variability. Remarkably, less abundant host species supported higher parasite diversity and abundance, and network analyses showed overall low connectance, nestedness, and modularity, but higher modularity was observed in the most complex FPZ, suggesting that physical complexity enhances compartmentalization of biotic interactions. Our findings highlight the role of river geomorphology in shaping ecological networks and support the use of parasites as sensitive indicators of ecosystem structure and integrity under changing environmental conditions.</p>