This study investigated background levels and uptake rates of organophilic metals, particularly selenium, in ten streams draining portions of the Yukon-Tanana Terrane and Cassiar Platform between Ross River and Watson Lake, Yukon. The study area is suspected to have elevated background metals concentrations and is of interest for mineral exploration and development due to high mineralization. Information on natural metals levels is lacking for this region and for the Yukon in general. Water, sediments, benthic invertebrates and fish (slimy sculpin; Cottus cognatus) were sampled and analyzed for metals concentrations. Benthic invertebrates were identified to genus and percent composition of each species in each stream was calculated. The lack of anthropogenic activity in the area indicates that selenium concentrations found in all sample media and natural, background concentrations. Of all the sample media, concentrations of selenium were highest in sediment; however, sediment selenium concentrations were found to be in a range similar to levels documented at the Kudz Ze Kayah and Viceroy Brewery Creek mines in other regions of the Yukon. Selenium concentrations in water generally exceeded CCME guidelines, but also fell within a range similar to the Kudz Ze Kayah and Viceroy Brewery Creek mines. These findings with respect to selenium levels in water and stream sediments highlight the importance of developing site-specific selenium guidelines for management of aquatic systems. The rate of uptake of selenium in benthic invertebrate and fish tissues was greater than that of the other organophilic metals investigated. Selenium concentrations were generally higher in benthic invertebrates than in fish, likely owing to the detritus-feeding and bottom-dwelling life history of these invertebrates. Weak positive trends were noted in the relationship between selenium concentrations in fish and benthic invertebrates, and between fish and the water column. A significant positive relationship was noted between selenium concentrations in fish and stream sediments. These findings are consistent with past studies documenting dietary sources as the most common uptake pathways for selenium, with water comprising a secondary source. Examination of benthic invertebrate community composition revealed commonly abundant species and species typical of fast-flowing streams with high water quality, which is characteristic of the streams in the study area. The findings of this study provide valuable baseline information on background concentrations of metals, particularly selenium, as well as documentation of benthic invertebrate community composition, in an aquatic system that may experience resource development in the future.