Thawing of permafrost and a shift in the timing of major seasonal transitions (spring melt and fall freeze-up) are two anticipated effects of climate warming in northern regions. These fundamental changes in terrestrial ecosystems could have major ramifications for the timing and fluxes of carbon and nutrient exports from watersheds and the geochemical signatures of northern rivers. Discontinuous permafrost, which underlies watersheds in Interior Alaska (USA), is expected to degrade rapidly in response to climate warming and this will likely alter subsurface flows and flow paths, water residence times, water-soil, and water-rock interactions. This study of the Chena River in Interior Alaska was undertaken to quantify dissolved organic carbon (DOC), total dissolved nitrogen (TDN), major ion, strontium isotope, and stable oxygen and hydrogen isotope values during two year-long time series sampling periods. Our goal was to identify the hydrogeochemical signatures associated with the major seasonal flow regimes. Periods of increased discharge such as spring melt and major summer precipitation events yielded elevated DOC and TDN concentrations, diluted major ion concentrations, and shifted stable oxygen and hydrogen isotope ratios from base flow toward precipitation values. During dry summer periods nutrient concentrations decreased and strontium isotope values were indicative of a higher proportion of silicate versus carbonate mineral dissolution. Winter base flow had a unique geochemical signal with a slight increase in TDN concentrations compared to typical summer conditions, and a lower proportion of silicate versus carbonate mineral dissolution. Since flow paths in subarctic watersheds can change dramatically over the course of a year we interpreted our results within the context of a schematic model for subsurface flow to identify how permafrost degradation might affect nutrient exports and hydrogeochemical patterns in these watersheds.