Myxobolus cerebralis, the myxozoan parasite responsible for whirling disease in salmonid fishes, has a complex life-cycle involving an invertebrate host and 2 spore stages. Water flow rate is an environmental variable thought to affect the establishment and propagation of M. cerebralis; however, experimental data that separates flow effects from those of other variables are scarce. To compare how this parameter affected parasite infection dynamics and the invertebrate and vertebrate hosts, dead, infected fish were introduced into a naïve habitat with susceptible hosts under 2 experimental flow regimes: slow (0·02 cm/s) and fast (2·0 cm/s). Throughout the 1-year study, uninfected fry were held in both systems, the outflows were screened weekly for spores and the annelid populations were monitored. We found clear differences in prevalence of infection in the worms, prevalence and severity of infection in the fish, and host survival. Both flows provided environments in which M. cerebralis could complete its life-cycle; however, both the parasite and its invertebrate host proliferated to a greater extent in the slow flow environment over the 1-year study period. This finding is of significance for aquatic systems where the flow rate can be manipulated, and should be incorporated into risk analysis assessments.