Advancements in medical research increasingly demonstrate the critical and complex role of the microbiome in human health. However, relatively little research applies these innovations to conservation and natural resource management. Managers need tools for monitoring species health under rapidly changing environmental conditions, especially in freshwater systems where extinction rates are four times higher than terrestrial systems. The microbiome is a promising tool for understanding how habitat conditions influence animal health. We utilized field and laboratory experiments and next generation sequencing techniques to study the impact of water temperature, food availability, and habitat type on the skin and gut microbiome of juvenile Chinook salmon. Chinook salmon are a culturally, ecologically, and economically important species experiencing habitat loss and population declines. Results will provide a foundation for future microbiome research and may inform salmon management.