We chose a hypolimnetic-release tailwater of the San Juan River, New Mexico, to characterize the etiology of whirling disease, a parasitic infection of salmonids. We sampled a 2-km reach of the tailwater in August and December 2001 and June 2002 to characterize environmental factors influencing the distribution and density of Tubifex tubifex lineages and Myxobolus cerebralis infection rates. Shortly after the scouring flow, organic matter in sediments and T. tubifex densities increased within deep habitats. In contrast, no differences were observed in T. tubifex densities and organic matter collected from shallow habitats throughout the three sampling dates. Within this study area, we found three sympatric lineages of T. tubifex (lineages I, III, and VI). Lineage VI dominated riffle reaches, whereas lineages I, III, and VI were observed in pool habitats. Myxobolus cerebralis infection rates were higher in T. tubifex collected in pool habitats (3.01%) than in those collected in riffle habitats (0.51%). Only lineage III exhibited infection with M. cerebralis. We suggest that the habitat and genotype of T. tubifex are important in characterizing prevalence of disease within the San Juan River tailwater. Scouring flow may have a beneficial effect on disease severity in salmonid hosts by reducing organic loading and hence T. tubifex abundance in deep habitats.