Experimental and ambient warming of Arctic tundra results in emissions of greenhouse gases to the atmosphere, contributing to a positive feedback to climate warming. Estimates of gas emissions from lakes and terrestrial tundra confirm the significance of aquatic fluxes in greenhouse gas budgets, whereas few estimates describe emissions from fluvial networks. We measured dissolved gas concentrations and estimated emissions of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) from water tracks, vegetated depressions that hydrologically connect hillslope soils to lakes and streams. Concentrations of trace gases generally increased as ground thaw deepened through the growing season, indicating active production of greenhouse gases in thawed soils. Wet antecedent conditions were correlated with a decline in CO2 and CH4 concentrations. Dissolved N2O in excess of atmospheric equilibrium occurred in drier water tracks, but on average water tracks took up N2O from the atmosphere at low rates. Estimated CO2 emission rates for water tracks were among the highest observed for Arctic aquatic ecosystems, whereas CH4 emissions were of similar magnitude to streams. Despite occupying less than 1% of total catchment area, surface waters within water tracks were an estimated source of up to 53–85% of total CH4 emissions from their catchments and offset the terrestrial C sink by 5–9% during the growing season. Water tracks are abundant features of tundra landscapes that contain warmer soils and incur deeper thaw than adjacent terrestrial ecosystems and as such might contribute to ongoing and accelerating release of greenhouse gases from permafrost soils to the atmosphere.