<p>The ecological effects of invasive species on native freshwater fauna and on free-living community structure have been widely documented, yet the role of parasite co-invasion in shaping host–parasite dynamics within river ecosystems remains comparatively understudied. Rivers in central–southern Chile offer a valuable natural setting to investigate these processes because they harbor varying proportions of invasive fish, mainly from the families Salmonidae and Poeciliidae. Invasion intensity changes predictably among basins and along river segments and native fish assemblages are species-poor and highly endemic. This combination provides a suitable context to detect parasite transmission pathways and potential host shifts with high resolution. We documented varying degrees of parasite richness, abundance and network connectance in native fish hosts in assessed rivers, while most invasive species showed low parasitic infections. The acanthocephalan parasite <i>Pomphorhynchus</i> sp. was identified as the only native parasite infesting salmonids, demonstrating a spillback mechanism (invasive species becoming competent hosts for native parasites, thereby amplifying the transmission of those parasites and indirectly increasing infection pressure on native hosts). Furthermore, as invasive fish abundance increased, parasite richness, parasite abundance, and network connectance in native fish and lampreys declined, suggesting transmission interference. This pattern was consistent regardless of river basin or functional process zone i.e., segment of a river network characterised by distinct hydrogeomorphic and ecological properties, indicating that the negative impact of invasive hosts on parasite communities operates independently of broader spatial or geomorphological differences. These findings highlight the complex effects of biological invasions on host-parasite dynamics, altering transmission networks and potentially reshaping native ecological interactions within river ecosystems.</p>