In continuously-flooded paddies, the small, fast-growing aquatic plant duckweed (Lemna minor L.) considered to compete with rice for nitrogen, thereby having a negative impact on early rice growth. While duckweed overpopulation was known can be effectively overcome through field water management, the influence of such management on the N fate and its use efficiency in rice-duckweed systems is poorly documented. Accordingly, a three-year (2020–2022) field experiment was conducted to examine the combined impact on rice yield, as well as N loss and utilization, of two water management approaches (flood irrigation, FI vs. alternate wetting and drying irrigation, AWD), factorially combined with two rice production systems (rice-duckweed, +D, vs. duckweed-free rice, -D). In AWD+D fields, the density of duckweed generally remained below 250 g m−2 (about 85 % coverage), whereas in FI+D fields it reached 100 % coverage (300 g m−2) within 5 days after transplanting, with individual duckweeds overlapping one another. Following AWD irrigation, duckweed performed as a nitrogen “cache,” akin to a split fertilizer application, with the first of several splits occurring at the rice crop's early tillering stage. Within the first 2 days of a specific wet-dry cycle, duckweed can store 0.5–1.5 g N m−2, and then, within a further 3 days, release 0.3–1.0 g N m−2. In contrast, in FI+D paddies, this caching function occurred once under mid-season drainage, with further N being stored in the duckweeds during the remaining rice production season. As a result, at harvest the 0–0.10 m soil layer's N level increased significantly (p<0.05) in both FI+D (8.5–16.8 %) and AWD+D (14.9–20.8 %) compared to FI-D and AWD-D, respectively. Due to the coverage and storage-release function of duckweed, apparent N loss decreased in rice-duckweed system by 1.4–12.5 % in the FI field and 22.1–31.3 % in the AWD field compared to their respective duckweed-free systems. In FI fields, except for a 10 % relative reduction in nitrogen recovery efficiency (NRE) in 2020, duckweed didn't significantly affect rice yield or NRE. The yield reduction (3.5–6.7 %) and the NRE increase (0.8–7.4 %) under AWD-D (vs. FI-D) was, in the presence of duckweed, compensated for and overrun, resulting in a greater yield (5.3–6.7 %) and NRE (5.4–28.9 %) in the AWD+D vs. AWD-D field. When duckweed was present, AWD irrigation improved the by-path nitrogen cycling through duckweed, making the AWD+D system more beneficial for rice cultivation and the agroecosystem's environment health. The AWD+D system offers a promising measure for building an efficient and sustainable rice-duckweed agroecosystem.