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Permafrost thaw is projected to restructure the connectivity of surface and subsurface flow paths, influencing export dynamics of dissolved organic matter (DOM) through Arctic watersheds. Resulting shifts in flow path exchange between both soil horizons (organic‐mineral) and landscape positions (hillslope‐riparian) could alter DOM mobility and molecular‐level patterns in chemical composition. Using conservative tracers, we found relatively rapid lateral flows occurred across a headwater Arctic tundra hillslope, as well as along the mineral‐permafrost interface. While pore waters collected from the organic horizon were associated with plant‐derived molecules, those collected from permafrost‐influenced mineral horizons had a microbial origin, as determined by fluorescence spectroscopy. Using high‐resolution nuclear magnetic resonance spectroscopy, we found that riparian DOM had greater structural diversity than hillslope DOM, suggesting riparian soils could supply a diverse array of compounds to surface waters if terrestrial‐aquatic connectivity increases with warming. In combination, these results suggest that integrating DOM mobilization with its chemical and spatial heterogeneity can help predict how permafrost loss will structure ecosystem metabolism and carbon‐climate feedbacks in Arctic catchments with similar topographic features.