Manayunkia speciosa is the obligate invertebrate host of Ceratonova (syn Ceratomyxa) shasta (Myxozoa), the parasite that causes ceratomyxosis (enteronecrosis) in salmon and trout. High peak discharge has been correlated with reduced ceratomyxosis in salmon hosts but how it may influence parasite dynamics in the invertebrate host is unknown. We sampled M. speciosa populations from three sections of the Klamath River, California, in spring and summer months in 2006, a water year that was characterized by i) winter and spring discharge equivalent in magnitude to a 10 year flood and ii) low risk of ceratomyxosis for salmon. M. speciosa were observed in all river sections and months but densities were highest in the upper section, where peak discharge was lowest. Populations were dominated by immature individuals in all river sections and months, followed by progeny and mature individuals. Prevalence of C. shasta infection was 0.25% (SE 0.09) in June; 0.13% (SE 0.09) in July; 0% (SE 0) in August, and 0.03% (SE 0.02) in September. This study provides baseline data on the density and size structure of M. speciosa populations and the prevalence of C. shasta infection following a high magnitude flood event. We discuss the results in the context of using flow manipulation as a tool for managing ceratomyxosis.