This study aimed to better understand the stabilisation of rice rhizodeposition in paddy soil under the interactive effects of different N fertilisation and water regimes. We continuously labelled rice ('Zhongzao 39') with (CO2)-C-13 under a combination of different water regimes (alternating flooding-drying vs. continuous flooding) and N addition (250 mg N kg(-1) urea vs. no addition) and then followed C-13 incorporation into plant parts as well as soil fractions. N addition increased rice shoot biomass, rhizodeposition, and formation of C-13 (new plant-derived C) in the rhizosphere soils under both water regimes. By day 22, the interaction of alternating flooding-drying and N fertilisation significantly increased shoot and root C-13 allocations by 17 and 22%, respectively, over the continuous flooding condition. The interaction effect also led to a 46% higher C-13 allocation to the rhizosphere soil. Alone, alternating water management increased C-13 deposition by 43%. In contrast, N addition increased C-13 deposition in rhizosphere soil macroaggregates under both water regimes, but did not foster macroaggregation itself. N treatment also increased C-13 deposition and percentage in microaggregates and in the silt and clay-size fractions of the rhizosphere soil, a pattern that was higher under the alternating condition. Overall, our data indicated that combined N application and a flooding-drying treatment stabilised rhizodeposited C in soil more effectively than other tested conditions. Thus, they are desirable practices for improving rice cropping, capable of reducing cost, increasing water use efficiency, and raising C sequestration.