Soils derived from black shale can accumulate high concentrations of elements of environmental concern, especially in regions with semiarid to arid climates. One such region is the Colorado River basin in the southwestern United States where contaminants pose a threat to agriculture, municipal water supplies, endangered aquatic species, and water-quality commitments to Mexico. Exposures of Cretaceous Mancos Shale (MS) in the upper basin are a major contributor of salinity and selenium in the Colorado River. Here, we examine the roles of geology, climate, and alluviation on contaminant cycling (emphasis on salinity and Se) during weathering of MS in a Colorado River tributary watershed. Stage I (incipient weathering) began perhaps as long ago as 20 ka when lowering of groundwater resulted in oxidation of pyrite and organic matter. This process formed gypsum and soluble organic matter that persist in the unsaturated, weathered shale today. Enrichment of Se observed in laterally persistent ferric oxide layers likely is due to selenite adsorption onto the oxides that formed during fluctuating redox conditions at the water table. Stage II weathering (pedogenesis) is marked by a significant decrease in bulk density and increase in porosity as shale disaggregates to soil. Rainfall dissolves calcite and thenardite (Na2SO4) at the surface, infiltrates to about 1 m, and precipitates gypsum during evaporation. Gypsum formation (estimated 390 kg m−2) enriches soil moisture in Na and residual SO4. Transpiration of this moisture to the surface or exposure of subsurface soil (slumping) produces more thenardite. Most Se remains in the soil as selenite adsorbed to ferric oxides, however, some oxidizes to selenate and, during wetter conditions is transported with soil moisture to depths below 3 m. Coupled with little rainfall, relatively insoluble gypsum, and the translocation of soluble Se downward, MS landscapes will be a significant nonpoint source of salinity and Se to the Colorado River well into the future. Other trace elements weathering from MS that are often of environmental concern include U and Mo, which mimic Se in their behavior; As, Co, Cr, Cu, Ni, and Pb, which show little redistribution; and Cd, Sb, V, and Zn, which accumulate in Stage I shale, but are lost to varying degrees from upper soil intervals. None of these trace elements have been reported previously as contaminants in the study area.