Understanding the transport of inorganic mercury (Hg) and the bioaccumulative neurotoxin methylmercury (MeHg) from land into coastal waters is essential for the people and wildlife of the Arctic. Here, we conducted a multiyear study of dissolved total Hg (THg) and MeHg inputs to an Arctic coastal lagoon and present the first submarine groundwater discharge (SGD) flux estimates for Hg species in the Arctic, along with surface water fluxes. Rivers dominate dissolved Hg inputs to the lagoon during spring, but decline quickly following the spring freshet. Summertime SGD THg inputs are half that of river and runoff inputs at 500 ± 220 μmol d-1 km-1, decreasing to 270 ± 100 μmol d-1 km-1 in the autumn. Summertime SGD inputs of MeHg exceed springtime maximum riverine inputs to the lagoon, averaging 320 ± 130 μmol d-1 km-1, followed by a decline to negligible levels by late autumn. These results demonstrate that SGD could be the dominant source of MeHg into coastal Arctic waters following the spring freshet, highlighting a need to revisit the Arctic Hg and MeHg budgets, particularly as warming increases groundwater mobilization and methylation of Hg.