The Hells Canyon Complex (HCC) along the Snake River (Idaho-Oregon border, USA) encompasses three successive reservoirs that seasonally stratify, creating anoxic conditions in the hypolimnion that promote methylmercury (MeHg) production. This study quantified seasonal dynamics and interannual variability in mercury concentrations (inorganic divalent mercury (IHg) and MeHg) and loads at four reservoir inflow and outflow locations through the HCC (2014-2017). We observed (1) that the HCC is a net sink for both IHg and MeHg, (2) interannual variability in IHg and MeHg loads largely reflecting streamflow conditions, and (3) seasonal variability in particulate IHg loading at the inflow (greatest from February to April) and MeHg export from the outflow (greatest from September to December) of the HCC. Seasonal export of MeHg was evidenced by increases in monthly mean concentrations of unfiltered MeHg (approximately twofold) and the percentage of total mercury (THg) as MeHg (≥ fourfold) coincident with reservoir destratification. Despite evidence of seasonal export of MeHg from the HCC, annual loads indicate a 42% decrease in unfiltered MeHg from HCC inflow to outflow. Results from this study improve the understanding of seasonal variability in mercury transport through and transformation within a reservoir complex.