Sulfur (S) is an essential macronutrient and important component of the earth’s crust, and its cycling has critical impacts on trace metal mobility, water quality, and human health. Pyrite weathering is the primary pathway by which sulfur enters surface waters. However, biogeochemical cycling of sulfur in soils and the river corridor mediates sulfate exports. In this study, we identified the major forms of sulfur across multiple compartments and scales in a pristine mountainous watershed, including shale bedrock weathering profiles, hillslope soils, and alluvial floodplain sediments, in order to provide insight into biogeochemical sulfur cycling in a hydrologically variable alpine system. X‐ray absorption near‐edge spectroscopy (XANES) analysis of shale weathering profiles showed clear evidence of pyrite oxidation to sulfate, with large accumulations of intermediate S(0) (20%–53%). Micro‐scale XANES showed evidence of reprecipitation of pyrite at fracture surfaces within the permanently saturated zone. Organic sulfur dominated S speciation in shallow hillslope soil and floodplain sediment, with little evidence of reduced inorganic S. However, mackinawite formation, representing active sulfate reduction, was observed in saturated oxbow sediments and saturated weathered shale underlying floodplain sediments. Further evidence of sulfate reduction from aqueous sulfur isotopic analysis was observed in shallow groundwater transects across an Fe‐reducing meander, whereas increases in pore water sulfate concentrations implied sulfur oxidation at other locations. The data present an integrated picture of sulfur cycling in a shale‐dominated watershed, where riverine sulfate exports are mediated by biological cycling, particularly in redox‐stratified and temporally dynamic hyporheic zone sediments.