The Cinnabar and Fern mine sites in central Idaho are primary source areas for elevated mercury and arsenic entering the South Fork of the Salmon River, which provides critical spawning habitat for bull trout and Chinook salmon. Mercury mineralization is hosted by carbonate rocks, which generate waters dominated by Ca2+ and HCO3 - at pH 7 to 9. A synoptic sampling was conducted on headwater tributaries to determine geologic background concentrations and quantify trace metal concentrations in stream water associated with historical mining. Geologic background concentrations in unfiltered Cinnabar Creek water were 8 - 14 ng Hg L-1 and 4.8 - 9.5 µg As L-1. Immediately downstream from the mine site, concentrations increased to 257 ng Hg L-1 and 20.6 µg As L-1. Groundwater inflow diluted these concentrations by approximately half before the confluence of Cinnabar Creek with Sugar Creek. As expected, mercury and arsenic concentrations increased downstream in Sugar Creek below the confluence with Cinnabar Creek. However, the final downstream reach on Sugar Creek showed an increase in unfiltered mercury, methylmercury, and iron concentrations relative to the upstream reach. This increase is associated with historical mining activity in a mineralized area of carbonate rock that intersects the reach.