Biogeochemical cycling of N and S was examined at two watersheds in the Adirondack Mountains, New York, to better understand the retention and loss of these elements during winter and spring snowmelt. We analyzed stable isotope compositions of NO3- (δ15N-NO3-, δ18O-NO3-) and SO42- (δ34S-SO42-, δ18O-SO42-), along with concentrations and fluxes of NO3- and SO42-, in precipitation, throughfall, snowpack, snowmelt, soil water, groundwater, and stream water. Isotopic results showed no evidence of NO3- and SO42- transformations in the forest canopy and snowpack; however, markedly decreased δ18O values of NO3- and SO42- in forest floor water suggest that microbial processing occurred in organic soil horizons. Similarly low δ18O values of NO3- and SO42- were observed in forest floor and mineral soil leachates, groundwater, and streams. Over the winter observation period, most of the NO3- and SO42- in stream water was from a watershed-derived source, whereas atmospheric contributions were relatively minor. Despite differences in soil water NO3- concentrations between watersheds, the isotopic composition of NO3- (δ15N-NO3-, δ18O-NO3-) was similar, and indicated that in both watersheds most of the NO3- was produced by nitrification in the forest soils. Although there was likely some contribution of SO42- from microbial oxidation of carbon-bonded sulfur, most of the stream water SO42- appeared to be derived from weathering of S-containing bedrock or parent material. The decreased δ18O values of NO3- and SO42- in upper soil horizons indicate that atmospheric deposition of N and S was not directly linked with stream water losses, even during winter and spring snowmelt.