In high-latitude catchments where permafrost is present, runoff dynamics are complicated by seasonal active-layer thaw, which may cause a change in the dominant flowpaths as water increasingly contacts mineral soils of low hydraulic conductivity. A 2-year study, conducted in an upland catchment in Alaska (USA) underlain by frozen, well-sorted eolian silt, examined changes in infiltration and runoff with thaw. It was hypothesized that rapid runoff would be maintained by flow through shallow soils during the early summer and deeper preferential flow later in the summer. Seasonal changes in soil moisture, infiltration, and runoff magnitude, location, and chemistry suggest that transport is rapid, even when soils are thawed to their maximum extent. Between June and September, a shift occurred in the location of runoff, consistent with subsurface preferential flow in steep and wet areas. Uranium isotopes suggest that late summer runoff erodes permafrost, indicating that substantial rapid flow may occur along the frozen boundary. Together, throughflow and deep preferential flow may limit upland boreal catchment water and solute storage, and subsequently biogeochemical cycling on seasonal to annual timescales. Deep preferential flow may be important for stream incision, network drainage development, and the release of ancient carbon to ecosystems