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Many freshwater habitats are subject to change through time. Specifically, natural flow regimes are substantially modified by not only seasonal climatic change, but also anthropogenic activity. Consequently, freshwater organisms are exposed to variable flow, potentially altering their behaviour and subsequently parasite transmission amongst social hosts. Here, we investigate the effects of flow conditions on the shoaling behaviour of Trinidadian guppies (Poecilia reticulata), and the resulting transmission of a directly transmitted ectoparasite, Gyrodactylus turnbulli. Shoals exposed to continuous flow exhibited significantly greater G. turnbulli peak intensities and abundance when compared to fish subjected to interrupted, but not no-flow conditions. Parasite transmission rate was greater in shoals exposed to interrupted flow, resulting in parasites becoming more distributed amongst shoal members and thus reducing mean intensity in comparison to continuous flow shoals. Furthermore, as prevalence increased, the distance between shoaling conspecifics increased at greater rates in interrupted and no-flow conditions compared to continuous flow: indicating that in the absence of flowing water, parasitism has a greater effect on shoaling decisions. This data highlights how fish behaviourally respond to variable flow conditions and the implications for parasite transmission.