Little information exists about sources and sinks of greenhouse gases (GHGs) to account for net emissions from agroecosystems. We evaluated the effects of irrigation, tillage, crop rotation, and N fertilization on net global warming potential (GWP) and greenhouse gas intensity (GHGI) in a Lihen sandy loam from 2008 to 2011 in western North Dakota. Treatments were two irrigation practices (irrigated and non-irrigated) and five cropping systems [conventional-till malt barley (Hordeum vulgaris L.) with N fertilizer (CTBN), conventional-till malt barley with no N fertilizer (CTBO), no-till malt barley-pea (Pisum sativum L.) with N fertilizer (NTB-P), no-till malt barley with N fertilizer (NTBN), and no-till malt barley with no N fertilizer (NTBO)]. While CO₂ equivalents of irrigated, tilled, and N-fertilized treatments were greater than no irrigated, tilled, and N fertilized treatments, respectively, the equivalents of N₂O flux was greater in non-irrigated NTBN and CH₄ flux in irrigated CTBN than most other treatments. Previous year’s crop residue returned to the soil and C sequestration rate were greater in irrigated NTB-P but grain yield was greater in irrigated CTBN than other treatments. Net GWP and GHGI based on soil respiration were greater in irrigated NTBO but GWP and GHGI based on soil organic C (SOC) were greater in irrigated CTBN and CTBO than other treatments. Regardless of irrigation, NTB-P may be used to reduce net GHG emissions from malt barley production compared to other treatments in the northern Great Plains. This management option may also reduce energy and N inputs and incidences of weeds, pests, and diseases compared to conventional system (CTBN).