The Great Plains region of the United States is an agricultural production center for the global market and, as such, an important source of greenhouse gas (GHG) emissions. This article uses historical agricultural census data and ecosystem models to estimate the magnitude of annual GHG fluxes from all agricultural sources (e.g., cropping, livestock raising, irrigation, fertilizer production, tractor use) in the Great Plains from 1870 to 2000. Here, we show that carbon (C) released during the plow-out of native grasslands was the largest source of GHG emissions before 1930, whereas livestock production, direct energy use, and soil nitrous oxide emissions are currently the largest sources. Climatic factors mediate these emissions, with cool and wet weather promoting C sequestration and hot and dry weather increasing GHG release. This analysis demonstrates the long-term ecosystem consequences of both historical and current agricultural activities, but also indicates that adoption of available alternative management practices could substantially mitigate agricultural GHG fluxes, ranging from a 34% reduction with a 25% adoption rate to as much as complete elimination with possible net sequestration of C when a greater proportion of farmers adopt new agricultural practices.