- The waterborne, myxozoan parasite Ceratonova shasta is endemic to the Pacific Northwest and can be lethal to its secondary salmonid host, including the culturally, economically, and recreationally important spring Chinook salmon (Oncorhynchus tshawytscha) of the Deschutes River, OR. Previously described genotypes of C. shasta exhibit specificity with their salmonid hosts. As a first step toward managing C. shasta in the Deschutes River, the spatial and temporal distribution of this pathogen and its genotypes needed to be described. Historically, parasite prevalence was quantified by fish mortalities from sentinel surveys at 2-3 sites at different times of year on the Deschutes River mainstem. Herein I used water sampling and qPCR to provide a method for determining detailed spatiotemporal information about waterborne parasite distribution both within (Chapter 4) and between (Chapter 2) sites of the river. Ceratonova shasta was detected throughout the upper and lower Deschutes River basins at variable positions within sites. Though there was variation between years (average spores/L 81.0, 11.2, 46.4 in 2016, 2017, 2018, respectively), C. shasta density was 1.5x higher between rkm 48-82 than the average of all other spatial survey sites. Additionally, sites such as DRR (rkm 116) and DWS (rkm 155) had higher than average C. shasta abundance for 63% (5/8) of the surveys. Only low densities (< 1.5 spores/L) of C. shasta were detected in the Warm Springs River, an important spawning tributary for spring Chinook salmon. Using linear mixed effect models (LMEMs), parasite abundance at temporal monitoring sites in the lower basin appears to be positively related to water temperature but has an inverse relationship with river discharge, supporting previously described observations in the Klamath River, CA/OR. The upper Deschutes basin exhibited different temporal dynamics than the lower basin with variable peaks in July or August. In Chapter 3, I determined that C. shasta genotype I dominated the lower Deschutes River basin below Round Butte Dam, type II was the main genotype present in the upper basin above Round Butte Dam, and type O was detected throughout the system at lower proportions than I or II. Type II was also identified in the lower basin, but only during August. Genotype I was not detected in the upper basin, despite the passage of spring Chinook salmon above the Round Butte Dam for over a decade. I identified that peak C. shasta abundance and the Chinook salmon host-specific genotype I coincide with spring Chinook adult returns and juvenile spring Chinook releases, although spring Chinook salmon are one of the least abundant salmonid species. Genotype O is associated with Steelhead trout, the most abundant species of salmonid in the upper and lower basins of the Deschutes River. However, although genotype O was found throughout both basins, supporting earlier hypotheses that the spatial and temporal patterns of genotypes may be explained by host distribution, our hypothesis that the density of genotypes in water samples would be related to salmonid abundance was not supported. Despite the high densities of C. shasta genotype I in water samples of the lower Deschutes, only mild to moderate pathology was observed in juvenile and adult tissue samples (Appendix A). Although C. shasta was the most common pathogen that we detected and caused enteronecrosis, pathology associated with Renibacterium salmoninarum and Parvicapsula minibicornis was observed also in juvenile and adult spring Chinook salmon, respectively. Therefore, while C. shasta may be contributing to low survival of spring Chinook salmon in the lower Deschutes River basin, it does not appear to be the sole cause.