Permafrost plays an important role in shaping the chemistry of streams by restricting subsurface flows through catchments to soils. During the summer thaw of soil, subsurface flows migrate through deeper soil horizons presumably resulting in seasonal shifts in the inputs of carbon and nitrogen to the streams. Within streams, the extent of the hyporheic zone may also shift with seasonal thaw. Hyporheic zones have high mineralization and nitrification rates; thus expansion of the hyporheic zone throughout the season has important implications for stream chemistry. This study examined nitrogen cycling in two streams draining watersheds with varying extents of underlying permafrost to understand how nitrate uptake is affected as carbon sources shift during soil thaw. Additionally, we examined the extent of transient storage (hyporheic zone, eddies, pools) in order to determine if storage increases as the active layer thaws and if storage differs between the two streams. The research was conducted in two streams draining subcatchments with low and high permafrost extents (5% and 50% permafrost) of Caribou-Poker Creeks Research Watershed located in interior Alaska. Steady-state solute injections, amended with acetate and ¹⁵NO₃^-, were performed in both streams throughout the summer of 2008 to capture the seasonal thaw of soils. In the stream draining the low permafrost catchment, acetate uptake length was rapid initially, decreased to 2413 meters at mid-season, then further decreased to 2530 meters late in the season. In contrast, acetate uptake in the stream draining the higher permafrost watershed increased throughout the season from 3525 meters early in the season to 2073 meters late in the season. Addition of a labile carbon source appears to have stimulated nitrate uptake in the low permafrost stream initially but later there seems to have been nitrate production. The same pattern of nitrate uptake and possible production late in the season is evident in the high permafrost stream. The mass transfer coefficients (mm ml^-1) increase in both streams throughout the season indicating more carbon is being metabolized late in the season compared to early in the season; however, in general coefficients are two fold larger for the low permafrost stream compared to high permafrost stream. These contrasting patterns in carbon and nitrogen cycling have important implications for future functioning of streams as permafrost thaws, subsurface flows through watersheds change, and the resulting inputs of materials into streams is altered.