Nursery tanks and Burrows ponds at Dworshak National Fish Hatchery, Ahsahka, Idaho, containing age concentrate virus from water samples, IHN virus was detected in nursery tanks and Burrows ponds during the early stages of epizootics at concentrations ranging from 0.1 to 0.3 plaque-forming units (pfu)/mL. Peak virus concentrations were 1-5 pfu/mL in nursery tanks and exceeded 50 pfu/mL in Burrows ponds. When tangential flow filtration was used in conjunction with PEG precipitation, virus was detected in Burrows ponds at concentrations of 0.007-0.07 pfu/mL, 3-12 d before periods of rapidly increasing mortality. The results indicate that IHN epizootics begin with waterborne IHN virus at relatively low concentrations. Virus was not detected in the hatchery water supply, but waterborne virus can apparently be transmitted to susceptible populations even when the concentrations are below the threshold of detection for the methods used in this study.