Soil moisture strongly affects the balance between nitrification, denitrification and N 2 O reduction and therefore the nitrogen (N) efficiency and N losses in agricultural systems. In rice systems, there is a need to improve alternative water management practices, which are designed to save water and reduce methane emissions, but may increase N 2 O and decrease nitrogen use efficiency. In a field experiment with three water management treatments, we measured N 2 O isotopocule signatures (δ 15 N, δ 18 O and site preference, SP) of emitted and pore air N 2 O over the course of six weeks in the early rice growing season. Isotopocule measurements were coupled with simultaneous measurements of pore water NO 3 − , NH 4 + , dissolved organic carbon (DOC), water filled pore space (WFPS) and soil redox potential (Eh) at three soil depths. We then used the relationship between SP × δ 18 O-N 2 O and SP × δ 15 N-N 2 O in simple two endmember mixing models to evaluate the contribution of nitrification, denitrification, fungal denitrification to total N 2 O emissions and to estimate N 2 O reduction rates. N 2 O emissions were higher in a dry-seeded + alternate wetting and drying (DS-AWD) treatment relative to water-seeded + alternate wetting and drying (WS-AWD) and water-seeded + conventional flooding (WS-FLD) treatments. In the DS-AWD treatment the highest emissions were associated with a high contribution from denitrification and a decrease in N 2 O reduction; while in the WS treatments, the highest emissions occurred when contributions from denitrification/nitrifier-denitrification and nitrification/fungal denitrification were more equal. Modeled denitrification rates appeared to be tightly linked to nitrification and NO 3 − availability in all treatments, thus water management affected the rate of denitrification and N 2 O reduction by controlling the substrate availability for each process (NO 3 − and N 2 O), likely through changes in mineralization and nitrification rates. Our model estimates of mean N 2 O reduction rates match well those observed in 15 N fertilizer labeling studies in rice systems and show promise for the use of dual isotopocule mixing models to estimate N 2 losses.