Human manipulation of the sulfur (S) biogeochemical cycle has shifted dramatically in recent decades. Once dominated by fossil fuel emissions that caused inadvertent inputs of reactive S as acid deposition to forested ecosystems, our major pathway of S manipulation is now the multiple forms used in agriculture. While many decades of research have documented the consequences of atmospheric S deposition to acid-sensitive forest and aquatic ecosystems, comparatively little is known about the unintended consequences of its use in large-scale agricultural systems. This synthesis examines the inputs, transport, and ecological effects of S applications in agriculture. We describe case studies of three regional crops that use S in the United States: wine grapes in California, corn and soy in the Ohio River Valley, and sugarcane in Florida. Data from these areas demonstrate that as atmospheric S deposition has declined over time in response to federal regulation of emissions, agricultural S inputs have increased with expansion and intensification of crop systems, or in response to a decline in “free” atmospheric S deposition. Surface water sulfate export has declined about 2-5% per year over the past 30 years in areas of the northeastern U.S. historically impacted by acid rain and where crop systems are dispersed. Conversely, stream water sulfate concentrations have increased or remained elevated in the large agricultural areas represented by our case studies. In addition, we present highlights from detailed research in California wine grape systems that explores the utility of S stable isotopes for tracking agricultural S through complex watersheds, quantifying the forms and transformations of S, and determining their ultimate fates in downgradient aquatic ecosystems. Ultimately, there is a need to understand the implications of widespread agricultural S use and to develop science-stakeholder partnerships aimed at creating sustainable S management that reduces negative effects on local and adjacent ecosystems.