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Atmospheric deposition is a major source of the nutrients sulfur and selenium to agricultural soils. Air pollution control and cleaner energy production have reduced anthropogenic emissions of sulfur and selenium, which has led to lower atmospheric deposition fluxes of these elements. Here, we use a global aerosol-chemistry-climate model to map recent (2005–2009) sulfur and selenium deposition, and project future (2095–2099) changes under two socioeconomic scenarios. Across the Northern Hemisphere, we find substantially decreased deposition to agricultural soils, by 70 to 90% for sulfur and by 55 to 80% for selenium. Recent trends in sulfur and selenium concentrations in USA streams suggest that catchment mass balances of these elements are already changing due to the declining atmospheric supply. Sustainable fertilizer management strategies will need to be developed to offset the decrease in atmospheric nutrient supply and ensure future food security and nutrition, while avoiding consequences for downstream aquatic ecosystems.