While the importance of disease-induced mortality in wild fish populations has been purported, little research has investigated infectious agent dynamics in free-ranging fishes. The objective of this thesis was to investigate host-pathogen dynamics in three ecologically, culturally, and economically important salmonid species to characterize biological and environmental factors that mediate host response and survival associated with relative infection burden (RIB). To achieve this goal, a synthesis of the current state of wild fish epidemiology was conducted, with a focus on novel genomic techniques and ways in which they can be used to complement commonly employed fisheries field methods. High throughput qPCR and non-lethal gill biopsies were then used in three separate field studies to investigate RIB of microbial infectious agents and genetic biomarkers of host condition. To characterize the transcriptomic response of a long-lived, iteroparous salmonid to infectious agents and investigate the potential for invasive pathogens in Arctic waters, Arctic char from three separate populations were sampled during the fall migration, revealing site-specific differences in pathogen species richness and RIB, and provided new records for detection of likely endemic infectious agents. To investigate the influence of high water temperatures, Atlantic salmon were experimentally displaced downstream of a barrier and periodically sampled to track changes in infectious agent prevalence, relative infection burden, and host response over a 32 day period. Here, river temperature was significantly related to stress and immune biomarkers, while RIB was negatively associated with body condition. Finally, radio telemetry was used to track post-release survival and behaviour of coho salmon exposed to experimental fisheries stressors to characterize interactions between fisheries stress, host condition, and RIB. Fishery treatment and RIB were not associated with survival, however relative infection burden was associated with post-release behaviour in that high RIB began up-river migration post-release sooner than fish with lower RIB. The duration of handling alone was significantly related to mortality irrespective of fisheries treatment. Together, these findings demonstrate the diversity of factors associated with infectious agent communities and host response, and provide valuable information for the ongoing monitoring and investigation of wild salmonids.