We grew rice in phosphorus (P) deficient subtropical paddy soil in a field study and used ¹³CO₂ continuous labelling to investigate photosynthetic carbon (C) partitioning and allocation under FLOOD versus WET/DRY conditions, with and without P fertilization (80 mg P kg^-1). The plants and soil were sampled after each of three WET/DRY cycles to determine ¹³C allocation in above- and belowground plant biomass, microbial biomass, the rhizosphere, and bulk soil. Irrespective of water management, P-fertilized plants had higher biomass and P content and more total ¹³C in the rice-soil system, especially the ¹³C incorporation into the shoots (51%–96%), than samples without P fertilization. Root and bulk-soil ¹³C were largely independent of both P fertilization and water management. However, by the third sampling, P fertilization had increased the amount of ¹³C and microbial biomass ¹³C in the rhizosphere soil (RS) by 28% (WET/DRY) and 95% (FLOOD), and by 47% (WET/DRY) and 50% (FLOOD), respectively. The WET/DRY condition had significantly higher microbial biomass and ¹³C contents than FLOOD condition only in the RS. These results indicate that a well-established aboveground plant biomass following P fertilization is required to increase belowground C allocation. Thus, WET/DRY conditions, like FLOOD conditions, can provide moisture sufficient for unhindered P availability in rice-paddy system.