<p>Freshwater mussels in the order Unionida are a highly endangered taxon of ecosystem engineers with a variety of conservation and reintroduction efforts around the world attempting to increase wild populations. The unionid lifecycle involves a parasitic larval life-stage (glochidia), primarily adapted for dispersal rather than growth. Little is known about the behavioural effects of the glochidia on their host fish. We investigated the shoaling behaviour and habitat preference of the Eurasian minnow (<i>Phoxinus phoxinus</i>) while infested with the glochidia of one of Europe’s most endangered unionid mussels, the thick-shelled river mussel (<i>Unio crassus</i>). Behavioural assays were carried out in a hydrologically complex flow-through aquaria at two time points of the infestation period, a carrying stage and an excystment stage (14 and 28 days post infestation). We demonstrate that glochidiosis reduces minnow shoaling frequency and increases the number of isolated individuals. However, minnow shoal area and nearest neighbour distance remained unaffected. Infested minnows demonstrated a significant preference for slower flowing and less turbulent habitat. These results suggest that glochidiosis reduces host swimming efficiency, which likely increases predatory pressure on infested minnows. Simultaneously, this preference for calmer habitats may benefit the encysted mussels, as these habitats are better suited for juvenile mussel excystment. Our results highlight the importance of low-flow and low-turbulence habitats for unionid recruitment, as parasitized host individuals tolerate these conditions well.</p>