Rapid warming in the Arctic threatens to destabilize mercury (Hg) deposits contained within soils in permafrost regions. Yet current estimates of the amount of Hg in permafrost vary by ∼4 times. Moreover, how Hg will be released to the environment as permafrost thaws remains poorly known, despite threats to water quality, human health, and the environment. Here we present new measurements of total mercury (THg) contents in discontinuous permafrost in the Yukon River Basin in Alaska. We collected riverbank and floodplain sediments from exposed banks and bars near the villages of Huslia and Beaver. Median THg contents were 49+13/−21 ng THg g sediment−1 and 39+16/−18 ng THg g sediment−1 for Huslia and Beaver, respectively (uncertainties as 15th and 85th percentiles). Corresponding THg:organic carbon ratios were 5.4+2.0/−2.4 Gg THg Pg C−1 and 4.2 +2.4/−2.9 Gg THg Pg C−1. To constrain floodplain THg stocks, we combined measured THg contents with floodplain stratigraphy. Trends of THg increasing with smaller sediment size and calculated stocks in the upper 1 m and 3 m are similar to those suggested for this region by prior pan-Arctic studies. We combined THg stocks and river migration rates derived from remote sensing to estimate particulate THg erosional and depositional fluxes as river channels migrate across the floodplain. Results show similar fluxes within uncertainty into the river from erosion at both sites (95+12/−47 kg THg yr−1 and 26+154/−13 kg THg yr−1 at Huslia and Beaver, respectively), but different fluxes out of the river via deposition in aggrading bars (60+40/−29 kg THg yr−1 and 10+5.3/−1.7 kg THg yr−1). Thus, a significant amount of THg is liberated from permafrost during bank erosion, while a variable but generally lesser portion is subsequently redeposited by migrating rivers.