Objectives This study evaluated the feasibility of substituting conventional field nitrogen (N) fertilization with bowl seedling tray application, examining its impact on seedling quality, rice nutrient uptake, grain yield, and nutrient runoff into paddy surface water. The aim was to inform optimized N management strategies that minimize N and phosphorus (P) losses.

Methods A field trail was conducted in Guangxi Academy of Agricultural Sciences, with rice cultivar "Guiyefeng" as test materials. Three treatments were applied, CK: conventional seedling-raising and N fertilizer application rate (CK); T1: bowl seedlings, with 30% reduced N applied at a 4:6 ratio between nursery and tillering stages using coated urea (180-day release); T2: bowl seedlings, with 30% reduced N (coated urea) applied entirely within the bowls. Seedling quality (stem base width, leaf number, root length/number, aboveground biomass, N/P/K content) was assessed 17 days post-transplanting. Surface water samples were collected post-fertilization to measure N and P concentrations. At harvest, grain yield, yield components, and N/P/K accumulation in rice and straw were analyzed.

Results Both T1 and T2 significantly enhanced stem base width, leaf number, max. root length, root traits, aboveground biomass, and N content compared to CK. T2 outperformed T1 in most metrics, indicating superior seedling vigor. Compared to CK, T2 increased grain yield by 24.9% through increased panicle length and effective panicle number, enhanced N content of rice stalk, gain, and root by 20.4%, 16.0%, 31.2%, thus increased N accumulation rate of rice stalk and grain by 13.5% and 44.8%, respectively. T2 also surpassed T1 in grain yield (+18.1%), N content in rice stalk, rice and root (11.1%, 14.2%, 18.0%, respectively), and N accumulation rate of in grain (34.8%). T1, T2 and CK exhibited comparable P content in seedlings and P accumulation rate in rice straw and grain. T1 and T2 reduced total N and ammonium in surface water within 7 days after nursery fertilizer (vs. CK), T2 further reduced the total N and ammonium concentrations within 5 days after tiller fertilization (vs. CK and T1). Both T1 and T2 treatments reduced the cumulative loss of total N, ammonium, nitrate and total P by 84.3%−86.8%, 93.7%−95.7%, 51.5%−57.4% and 14.0%−30.2% in seedling stage, and the cumulative loss of total N and ammonium by 23.2%−68.6% and 32.2%−65.9% in tillering stage, with T2 treatment demonstrating the higher decrease.

Conclusions Applying 30% reduced N via coated urea entirely within bowl seedling trays effectively enhanced seedling quality, rice yield, and N uptake while minimizing surface water N concentrations throughout the growing season. This approach significantly curtails nutrient runoff, thereby reducing eutrophication risks and promoting sustainable rice cultivation.