Parasites are ubiquitous members of ecological communities, capable of contributing to the decline of vulnerable populations. Therefore, monitoring parasite level is a critical component for host management. Molecular tools, such as quantitative polymerase chain reaction (qPCR), can be valuable additions to monitoring protocols that assess parasitic disease risk to hosts. To be successful, monitoring protocols must capture biologically relevant environmental data, and relate that data to disease risk. This project assesses the application of molecular analysis of environmental water samples for monitoring the ciliate protozoan Ichthyophthirius multifiliis (Ich) in the Klamath River, CA. Ich is an economically and ecologically significant parasite of freshwater fishes, and has contributed to mortality of pre-spawning adult salmon throughout the Pacific Northwest, including in the Klamath River. Chapter 1 introduces the study site (the lower Klamath River, CA), host population of concern (Klamath River salmonids), parasite of interest (Ich), and primary molecular technique (qPCR). Chapter 2 describes the development and validation of a qPCR assay targeting the SSU rDNA of Ich, as well as the initial application of the assay to environmental water samples. Chapter 3 presents a field application of the sampling method. Chapters 2 and 3 demonstrate the assay’s potential to inform the management of Ich infections in the Klamath River. Chapter 4 compares the genetic variation of Ich isolates published in GenBank, and those collected from pet shops (OR) and natural rivers (CA) (primarily the Klamath River) at the cox1 and SSU gene loci. This research indicates that qPCR analysis of environmental water samples could be a valuable monitoring tool for waterborne Ich in the Klamath River.