Southeastern Alaska is a remote coastal-maritime ecosystem that is experiencing increased deposition of mercury (Hg) as well as rapid glacier loss. We conducted the first survey of total and methyl Hg concentrations in regional streams and biota in Southeastern Alaska. Overall, streams draining large wetland areas had higher Hg concentrations in water, mayflies, and juvenile salmon than those from glacially-influenced or recently deglaciated watersheds. Filtered methyl Hg was positively correlated with wetland abundance. Aqueous Hg occurred predominantly in the particulate fraction of glacier streams but in the filtered fraction of wetland-rich streams. Colonization by anadromous salmon in both glacier and wetland-rich streams may be contributing additional marine-derived Hg. The spatial distribution of Hg in the range of streams sampled shows that watersheds are variably, yet fairly predictably, sensitive to atmospheric and marine inputs of Hg.