Boreal soils in permafrost regions contain vast quantities of frozen organic material that is released to terrestrial and aquatic environments via subsurface flowpaths as permafrost thaws. Longer flowpaths may allow chemical reduction of solutes, nutrients, and contaminants, with implications for greenhouse gas emissions and aqueous export. Predicting boreal catchment runoff is complicated by soil heterogeneities related to variability in active layer thickness, soil type, fire history, and preferential flow potential. By coupling measurements of permeability, infiltration potential, and water chemistry with a stream chemistry end member mixing model, we tested the hypothesis that organic soils and burned slopes are the primary sources of runoff, and that runoff from burned soils is greater due to increased hydraulic connectivity. Organic soils were more permeable than mineral soils, and 25% of infiltration moved laterally upon reaching the organic-mineral soil boundary on unburned hillslopes. A large portion of the remaining water infiltrated into deeper, less permeable soils. In contrast, burned hillslopes displayed poorly defined soil horizons, allowing rapid, mineral-rich runoff through preferential pathways at various depths. On the catchment scale, mineral/organic runoff ratios averaged 1.6 and were as high as 5.2 for an individual storm. Our results suggest that burned soils are the dominant source of water and solutes reaching the stream in summer, whereas unburned soils may provide longer term storage and residence times necessary for production of anaerobic compounds. These results are relevant to predicting how boreal catchment drainage networks and stream export will evolve given continued warming and altered fire regimes.