The impact of management on global warming potential (GWP), crop production, and greenhouse gas intensity (GHGI) in irrigated agriculture is not well documented. A no‐till (NT) cropping systems study initiated in 1999 to evaluate soil organic carbon (SOC) sequestration potential in irrigated agriculture was used in this study to make trace gas flux measurements for 3 yr to facilitate a complete greenhouse gas accounting of GWP and GHGI. Fluxes of CO2, CH4, and N2O were measured using static, vented chambers, one to three times per week, year round, from April 2002 through October 2004 within conventional‐till continuous corn (CT‐CC) and NT continuous corn (NT‐CC) plots and in NT corn–soybean rotation (NT‐CB) plots. Nitrogen fertilizer rates ranged from 0 to 224 kg N ha−1 Methane fluxes were small and did not differ between tillage systems. Nitrous oxide fluxes increased linearly with increasing N fertilizer rate each year, but emission rates varied with years. Carbon dioxide efflux was higher in CT compared to NT in 2002 but was not different by tillage in 2003 or 2004. Based on soil respiration and residue C inputs, NT soils were net sinks of GWP when adequate fertilizer was added to maintain crop production. The CT soils were smaller net sinks for GWP than NT soils. The determinant for the net GWP relationship was a balance between soil respiration and N2O emissions. Based on soil C sequestration, only NT soils were net sinks for GWP. Both estimates of GWP and GHGI indicate that when appropriate crop production levels are achieved, net CO2 emissions are reduced. The results suggest that economic viability and environmental conservation can be achieved by minimizing tillage and utilizing appropriate levels of fertilizer.