In a river survey, Gammarus pulex amphipods both unparasitised and parasitised with the acanthocephalan Echinorhynchus truttae were distributed similarly with respect to flow regimen, tending to be more abundant in faster, shallower, riffle patches. However, there was a higher prevalence of parasitism in faster, shallower areas than in slower, deeper areas and abundance correlated with macrophyte coverage for unparasitised but not parasitised amphipods, indicating subtle differences in habitat usage. A laboratory 'patch' simulation indicated that parasitism influenced micro-distribution. There were higher proportions of unparasitised amphipods in/under stone substrates and within weed. In contrast, there were higher proportions of parasitised amphipods in the water column and at the water surface. As the experiment progressed, unparasitised but not parasitised amphipod habitat usage shifted from those micro-habitats above the substrate and in the water column to those in/under the substrates. Experiments also demonstrated that parasitised amphipods were more active and had a greater preference for illumination. Previous studies of the effects of acanthocephalan parasitism of amphipod hosts have focussed on how drift behaviour is altered, now we show that subtle differences in micro-habitat usage could translate to greatly increased vulnerability to fish predation. We discuss how aggregation of parasitised individuals within specific habitats could promote parasite transmission.