We predicted changes in yields and direct net soil greenhouse gas (GHG) fluxes from converting conventional to alternative management practices across one of the world's most productive agricultural regions, the Central Valley of California, using the DAYCENT model. Alternative practices included conservation tillage, winter cover cropping, manure application, a 25% reduction in N fertilizer input and combinations of these. Alternative practices were evaluated for all unique combinations of crop rotation, climate, and soil types for the period 1997-2006. The crops included were alfalfa, corn, cotton, melon, safflower, sunflower, tomato, and wheat. Our predictions indicate that, adopting alternative management practices would decrease yields up to 5%. Changes in modeled SOC and net soil GHG fluxes corresponded to values reported in the literature. Average potential reductions of net soil GHG fluxes with alternative practices ranged from -0.7 to -3.3 Mg CO(2)-eq ha(-1) yr(-1) in the Sacramento Valley and -0.5 to -2.5 Mg CO(2)-eq ha(-1) yr(-1) for the San Joaquin Valley. While adopting a single alternative practice led to modest net soil GHG flux reductions (on average -1 Mg CO(2)-eq ha(-1) yr(-1)), combining two or more of these practices led to greater decreases in net soil GHG fluxes of up to -3 Mg CO(2)-eq ha(-1) yr(-1). At the regional scale, the combination of winter cover cropping with manure application was particularly efficient in reducing GHG emissions. However, GHG mitigation potentials were mostly non-permanent because 60-80% of the decreases in net soil GHG fluxes were attributed to increases in SOC, except for the reduced fertilizer input practice, where reductions were mainly attributed to decreased N(2)O emissions. In conclusion, there are long-term GHG mitigation potentials within agriculture, but spatial and temporal aggregation will be necessary to reduce uncertainties around GHG emission reductions and the delivery risk of the associated C credits. (C) 2011 Elsevier B.V. All rights reserved.