Alternate wetting and drying (AWD) irrigation is projected to replace continuous flooding (CF) irrigation for rice production in parts of the Mekong delta area during the dry season. A dry season field experiment was conducted in Mekong delta alluvial soil to compare N cycle processes and agronomic parameters under AWD and CF water management schemes. N-15-labeled urea was applied in microplots to follow the fate of fertilizer N. The major loss of fertilizer N occurred through ammonia volatilization amounting to 21% and 13% of the applied N in the AWD and CF treatments, respectively. Ammonia volatilization was largely controlled by soil and floodwater pH which determined the NH3/NH4+ ratio. Irrespective of water management, 10-12% of the fertilizer N could be recovered from the top soil (0-15 cm) after harvest, whereas 10% of fertilizer N accumulated in deeper soil horizons (15-50 cm). Even though the loss of fertilizer N through nitrification-denitrification was 6 fold higher under AWD than CF (0.22 versus 0.04 g N m(-2)) it only removed 2.5% of the applied fertilizer and was thus quantitatively insignificant. Overall, net N mineralization and potential nitrification in the top soil were stimulated by the AWD treatment, whereas the difference in water management practice did not affect N uptake by the plants, aboveground biomass, or grain yield. Fertilizer N contributed only around 20% of the N uptake by the plants probably because the soil was rich in N, which was deposited during the preceding flooding season. Although based on data from one dry season crop only, our study indicates that future implementation of AWD irrigation is unlikely to adversely affect crop yields by loss of fertilizer N in intensive rice production systems in the Mekong delta. (C) 2012 Elsevier Ltd. All rights reserved.