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Greenhouse gas (GHG) emissions are fueling global climate change, with methane and nitrous oxide being the primary agricultural gases emitted. It has been shown that N2O emissions correlate to moisture content fluctuations; however, emissions from agricultural fields in the semiarid regions of the Southwest where rewetting events occur regularly are not well established. The scope of this study was to quantify GHG emissions in correlation to soil moisture fluctuations and fertilizer application. The study was conducted continuously in two pecan [Carya illinoinensis (Wangenh.) K. Koch] orchards between Aug. 2010 and Aug. 2011 on a sandy loam soil (La Mancha) and a silty clay loam soil (Leyendecker), both under normal management practices. The small chamber technique was used to measure GHGs. Emissions varied greatly throughout the year. The largest flux of CO2 at La Mancha and Leyendecker both occurred during a drying event immediately following an irrigation event: 84,642.49 μg·m−2·h−1 and 30,338.24 μg·m−2·h−1, respectively. The net CH4 flux at Leyendecker and La Mancha was close to zero with the largest emissions occurring during wetting events. Results showed that N2O emissions were maintained near the baseline except for the few days following an irrigation event. The largest emission peak at La Mancha occurred after irrigation and nitrogen application: 322.06 μg·m−2·h−1. The largest emission peaks of 26.37 and 1.13 μg·m−2·h−1 at Leyendecker and La Mancha, respectively, occurred after irrigation, nitrogen application, and tillage. Nitrogen application was the driving factor affecting N2O emissions at La Mancha, whereas soil moisture content was the driving factor at Leyendecker. Emission factors (EFs) at La Mancha and Leyendecker were 0.49% and 0.05%, respectively. A thorough accounting of GHG emissions is necessary for budgeting and identifying mitigation policy.