Nitrate (NO3–) export coupled with high inorganic nitrogen (N) concentrations in Alaskan streams suggests that N cycles of permafrost-influenced ecosystems are more open than expected for N-limited ecosystems. We tested the hypothesis that soil thaw depth governs inorganic N retention and removal in soils due to vertical patterns in the dominant N transformation pathways. Using an in situ, push–pull method, we estimated rates of inorganic N uptake and denitrification during snow melt, summer, and autumn, as depth of soil–stream flowpaths increased in the valley bottom of an arctic and a boreal catchment. Net NO3– uptake declined sharply from snow melt to summer and decreased as a nonlinear function of thaw depth. Peak denitrification rate occurred during snow melt at the arctic site, in summer at the boreal site, and declined as a nonlinear function of thaw depth across both sites. Seasonal patterns in ammonium (NH4+) uptake were not significant, but low rates during the peak growing season suggest uptake that is balanced by mineralization. Despite rapid rates of hydrologic transport during snow melt runoff, rates of uptake and removal of inorganic N tended to exceed water residence time during snow melt, indicating potential for retention of N in valley bottom soils when flowpaths are shallow. Decreased reaction rates relative to water residence time in subsequent seasons suggest greater export of inorganic N as the soil–stream flowpath deepens due to thawing soils. Using seasonal thaw as a proxy for longer term deepening of the thaw layer caused by climate warming and permafrost degradation, these results suggest increasing potential for export of inorganic N from permafrost-influenced soils to streams.