At high concentrations, mercury (Hg) presents significant ecological risks to wildlife. Long-range atmospheric transport of Hg emissions from temperate and tropical regions can lead to contamination even in remote areas, such as the Arctic. In aquatic systems, atmospheric deposition of inorganic Hg can undergo methylation, forming methylmercury (MeHg), a highly toxic and bioaccumulative compound. Emergent aquatic insects accumulate MeHg during their larval stage and transfer it to terrestrial ecosystems upon emergence as adults, potentially exposing terrestrial predators to contamination. This study quantified dipteran-mediated Hg flux—calculated as emergent dipteran biomass multiplied by MeHg concentration—in five ponds and one lake on the Pituffik Peninsula in the High Arctic of Northwest Greenland. Emergent dipterans were collected weekly over a six-week period (June–August 2023). Biomass and Hg concentrations varied across lentic ecosystems and dipteran taxa, leading to differences in dipteran-mediated Hg flux among ecosystems. A risk analysis indicated that insectivorous Snow Bunting (Plectrophenax nivalis) and Lapland Longspur (Calcarius lapponicus) chicks consuming emergent dipterans would not be exposed to Hg concentrations high enough to pose a risk to their health.