Information on the distribution and abundance of Myxobolus cerebralis triactinomyxons in natural systems is limited because direct and accurate sampling methods for this life stage have not been developed. Existing methods are based on indirect measures of triactinomyxon densities and are therefore confounded. Direct estimation of triactinomyxon concentrations would more exactly pinpoint the ambient infection risk to wild fish and allow evaluation of management strategies designed to mitigate the effects of the disease. We developed a mobile packed-bed filtration system that quickly, accurately, and precisely collects, concentrates, and quantifies triactinomyxons. The system includes pumping, prefiltration, two rounds of packed-bed filtration, and centrifugation. Laboratory tests of the completed system using known quantities of triactinomyxons resulted in a mean recovery rate of 91% with a minimum detectable concentration of triactinomyxons of 0.04/L. We subsequently field-tested the system at a site known to be positive for the parasite and recovered triactinomyxons at densities of 0.7-1.4/L. The packed-bed filtration system has the potential to quickly determine the temporal and spatial variation in infection risk and to test the efficacy of various management strategies.