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Parasites can indirectly affect ecosystem function by altering host phenotype, but the trait‐mediated impacts of parasitism at an ecosystem level remain poorly characterised. However, understanding the influence of parasites is central to understanding the ecosystem services provided by host species, especially in an era of global environmental change.We examined the effect of native (the trematode Rhipidocotyle campanula) and invasive (the bitterling fish Rhodeus amarus) parasites, and their interaction, on the clearance rates of unionid mussels, a dominant ecosystem‐engineering group that modify freshwater ecosystems worldwide. We used a combination of field experiments, laboratory experiments and ecological simulations to demonstrate the phenotypic impact of parasites on the functional response of two mussel species across an environmental gradient (suspended particle concentration), and extended this with host and parasite community data to demonstrate the consequences for a real‐world ecosystem, the Old West River in Cambridgeshire, England.Both parasites altered the clearance rates of their hosts but in contrasting fashion: while R. campanula increased host clearance rates relative to uninfected conspecifics under all conditions, R. amarus supressed clearance rates at high suspended particle concentrations (eutrophic conditions) but elevated them otherwise. The parasites displayed different infection patterns in the two host species, and the invasive R. amarus rarely co‐infected mussels with R. campanula.Given their disparate effects, the parasites' distributions reversed the relative filtration capacity of the two host species under high vs. low concentrations of suspended particles, demonstrating how differences between the infection patterns of native and invasive parasites, as well as their individual effects, need to be considered. Overall, the proportion of daily river discharge filtered by the combined mussel community changed by up to 96% in the presence of parasites. By incorporating multiple host species and multiple parasite species, we provide ecologically relevant evidence for the trait‐mediated effects of parasites on ecosystem processes.Our study demonstrates that parasitism can significantly alter wider ecosystem processes through changing the phenotype of their host. Future work on ecosystem function should take parasitism into account, and consider both trait‐mediated and density‐mediated effects. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]