A unique high temporal frequency data set from an irrigated cotton-wheat rotation was used to test the agroecosystem model DayCent to simulate daily N20 emissions from subtropical vertisols under different irrigation intensities. DayCent was able to simulate the effect of different irrigation intensities on N20 fluxes and yield, although it tended to overestimate seasonal fluxes during the cotton season. DayCent accurately predicted soil moisture dynamics and the timing and magnitude of high fluxes associated with fertilizer additions and irrigation events. At the daily scale we found a good correlation of predicted vs. measured N20 fluxes (r2 = 0.52), confirming that DayCent can be used to test agricultural practices for mitigating N20 emission from irrigated cropping systems. A 25-year scenario analysis indicated that N20 losses from irrigated cotton-wheat rotations on black vertisols in Australia can be substantially reduced by an optimized fertilizer and irrigation management system (i.e., frequent irrigation, avoidance of excessive fertilizer application), while sustaining maximum yield potentials.