We investigated surface-subsurface (hyporheic) exchange in two morphologically distinct arctic headwater streams experiencing warming (thawing) sub-channel conditions. Empirically parameterized and calibrated groundwater flow models were used to assess the influence of sub-channel thaw on hyporheic exchange. Average thaw depths were at least two-fold greater under the higher-energy, alluvial stream than under the low-energy, peat-lined stream. Alluvial hyporheic exchange had shorter residence times and longer flowpaths that occurred across greater portions of the thawed sediments. For both reaches, the morphologic (longitudinal bed topography) and hydraulic conditions (surface and groundwater flow properties) set the potential for hyporheic flow. Simulations of deeper thaw, as predicted under a warming arctic climate, only influence hyporheic exchange until a threshold depth. This depth is primarily determined by the hydraulic head gradients imposed by the stream morphology. Therefore, arctic hyporheic exchange extent is likely to be independent of greater sub-stream thaw depths.